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README.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8" />
<title>README.md - Grip</title>
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<link rel="stylesheet" href="/__/grip/static/octicons/octicons.css" />
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* GitHub Light v0.4.2
* Copyright (c) 2012 - 2017 GitHub, Inc.
* Licensed under MIT (https://github.com/primer/github-syntax-theme-generator/blob/master/LICENSE)
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<h3>
<span class="octicon octicon-book"></span>
README.md
</h3>
<article class="markdown-body entry-content" itemprop="text" id="grip-content">
<h1>
<a id="user-content-duplex-sequencing-pipeline" class="anchor" href="#duplex-sequencing-pipeline" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Duplex Sequencing Pipeline</h1>
<p>Brendan Kohrn, April 26, 2021<br>
Duplex Sequencing is copyright Scott Kennedy and Larwrence Loeb,
University of Washington, Seattle, WA, USA</p>
<h2>
<a id="user-content-table-of-contents" class="anchor" href="#table-of-contents" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Table of Contents:</h2>
<ol>
<li>Glossary</li>
<li>Dependencies</li>
<li>Setup</li>
<li>Genome Setup</li>
<li>Contaminant database setup</li>
<li>Bed and Interval_list file preparation</li>
<li>Configuration File creation</li>
<li>Recovery script creation</li>
<li>Running pipelines</li>
<li>Output file descriptions</li>
<li>Extra BAM tags:</li>
<li>Testing the pipeline</li>
<li>Full and partial reruns</li>
<li>Unlocking following a power failure</li>
</ol>
<h2>
<a id="user-content-1-glossary" class="anchor" href="#1-glossary" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>1: Glossary</h2>
<h3>
<a id="user-content-single-stranded-consensus-sequence-sscs" class="anchor" href="#single-stranded-consensus-sequence-sscs" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Single Stranded Consensus Sequence (SSCS)</h3>
<p>A construct created by comparing multiple reads and deciding ambiguities by
simple majority.</p>
<h3>
<a id="user-content-duplex-consensus-sequence-dcs" class="anchor" href="#duplex-consensus-sequence-dcs" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Duplex Consensus Sequence (DCS)</h3>
<p>A construct created by comparing two SSCSs.</p>
<h3>
<a id="user-content-family" class="anchor" href="#family" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>Family</h3>
<p>A group of reads that shares the same tag sequence.</p>
<h2>
<a id="user-content-2-dependencies" class="anchor" href="#2-dependencies" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>2: Dependencies:</h2>
<p>This pipeline is known to work with the following versions of
the following required programs:</p>
<ul>
<li>Python3.6+</li>
<li>Snakemake>=5.25.0</li>
<li>Pandas</li>
<li>Miniconda=4.7.*</li>
<li>bwa=0.7.17.* (for genome setup)</li>
<li>ncbi-blast=2.9.0 (installed separately, for contaminant database setup; note that while an older version can be used for database setup, a newer version CANNOT be used for database setup.)</li>
<li>mamba>=0.5.1 (needed for environment setup; install through conda)</li>
<li>wget (on macOS, install using homebrew; present by default on linux)</li>
</ul>
<p>Once Python3.6 is installed, snakemake and pandas can be installed using
pip3 or using whatever package manager you're using.
NOTE: For MacOS X, use the latest Snakemake. Blast can be downloaded in any of
several ways, including some package managers (Ubuntu: sudo apt-get install
ncbi-blast+). It can also be installed using conda if desired.</p>
<p>The recommended install method and order is:</p>
<ol>
<li>Install Miniconda</li>
<li>Use conda to install Python3 and Mamba</li>
<li>Use Mamba to install Snakemake, bwa, blast, and pandas, invoking both the
bioconda and conda-forge channels.</li>
</ol>
<h2>
<a id="user-content-3-setup" class="anchor" href="#3-setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>3: Setup:</h2>
<p>Find the location where you want the pipeline to be located and clone the
pipeline using git:</p>
<div class="highlight highlight-source-shell"><pre>git clone https://github.com/KennedyLabUW/Duplex-Seq-Pipeline.git</pre></div>
<p>change into the directory, and run:</p>
<div class="highlight highlight-source-shell"><pre>bash setupDS.sh MAX_CORES</pre></div>
<p>where MAX_CORES is the maximum number of cores you want the pipeline to
be able to use. This will create a test configuration file in the test
directory (test/testConfig.csv), a basic configuration file (DS_progConfig.yaml),
a run script (DS), a DAG-creation script (DS-dag), a reset script (DS-clean),
and an unlock script (DS-unlock).
After this, with the exception of setting up the Genomes
(See Section 4) and the (optional) blast contamination database (See
Section 5), you should be able to run the Duplex-Seq pipeline using</p>
<div class="highlight highlight-source-shell"><pre>bash /path/to/Duplex-Seq-Pipeline/DS CONFIG_CSV.csv</pre></div>
<p>where CONFIG_CSV.csv is a configuration CSV file generated as described
below.</p>
<p>If you want, you can also add the DS and DS-clean scripts to your path;
this will simplify invocation if you only have a single release version
on your system.</p>
<h2>
<a id="user-content-4-genome-setup" class="anchor" href="#4-genome-setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>4: Genome setup</h2>
<p>Put genomes in an easily findable location, such as our references
directory (i.e. ~/bioinformatics/reference).</p>
<p>Many genomes can be downloaded from UCSC
(<a href="http://hgdownload.soe.ucsc.edu/downloads.html" rel="nofollow">http://hgdownload.soe.ucsc.edu/downloads.html</a>). In order to download
genomes from there, you will need to download the twoBitToFa program from
the appropriate Utilities directory. twoBitToFa has the following syntax
(Copied from UCSC):</p>
<pre><code>twoBitToFa - Convert all or part of .2bit file to fasta
usage:
twoBitToFa input.2bit output.fa
options:
-seq=name Restrict this to just one sequence.
-start=X Start at given position in sequence (zero-based).
-end=X End at given position in sequence (non-inclusive).
-seqList=file File containing list of the desired sequence names
in the format seqSpec[:start-end], e.g. chr1 or chr1:0-189
where coordinates are half-open zero-based, i.e. [start,end).
-noMask Convert sequence to all upper case.
-bpt=index.bpt Use bpt index instead of built-in one.
-bed=input.bed Grab sequences specified by input.bed. Will exclude introns.
-bedPos With -bed, use chrom:start-end as the fasta ID in output.fa.
-udcDir=/dir/to/cache Place to put cache for remote bigBed/bigWigs.
Sequence and range may also be specified as part of the input file name using the syntax:
/path/input.2bit:name
or
/path/input.2bit:name
or
/path/input.2bit:name:start-end
</code></pre>
<p>Once you have downloaded a genome and converted it into FASTA format, it
needs to be indexed. To do this, open a terminal and navigate to your
the directory containing your genome. Note that in the following commands,
the word "genome.fasta" should be replaced with the file name of your
genome. These commands <strong>must</strong> be run in the same directory as the
reference genome</p>
<pre><code> bwa index genome.fasta
samtools faidx genome.fasta
# /Path/To/PicardTools should be the path to wherever you put your picard tools jar file.
# Also, genome.dict should match the name of your fasta (e.g. hg19.fasta to hg19.dict)
java -jar /Path/To/PicardTools/picard.jar CreateSequenceDictionary R=genome.fasta O=genome.dict
</code></pre>
<p>At the moment, this pipeline does not support compressed genomes.</p>
<h2>
<a id="user-content-5-contaminant-database-setup" class="anchor" href="#5-contaminant-database-setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>5: Contaminant Database Setup:</h2>
<p>The Duplex-Seq pipeline is designed to use a local NCBI Blast instance
to detect and remove potential contamination from non-target species and
identify issues arising from pseudogenes.
<em>This step is optional, but requires a valid NCBI Blast database file
name. To run without BLAST, enter "NONE" (with any capitalization)
in the blast_db field in the config.csv file.</em></p>
<p>To construct your contaminant database, if desired, first decide on a
list of species you want to monitor for contaminants. A suggested
starting list is:</p>
<ul>
<li>Human (hg38)</li>
<li>Mouse (mm10)</li>
<li>Rat (rn6)</li>
<li>C. elegens (ce11)</li>
<li>Yeast (sacCer3)</li>
<li>Fruit Fly (dm6)</li>
<li>Cow (bosTau9)</li>
<li>Dog (canFam3)</li>
</ul>
<p><strong>It is important that any genome you plan to use for alignment be included in this database,
in the same version (e.g. if your alignment genome uses UCSC chromosome
names, your genome in the database cannot use NCBI chromosome names, but
must also use UCSC chromosome names). It should also be noted that, while older versions of BLAST can be used for database setup, setup should use at the latest version 2.9.0; databases constructed with later BLAST versions may not work with the pipeline</strong>.</p>
<p>Database setup consists of two steps:</p>
<ol>
<li>Sub-database Creation:</li>
</ol>
<p>Create the database using:</p>
<pre><code>makeblastdb \
-dbtype nucl \
-title GENOME \
-out GENOME_db \
-in GENOME.fa \
-taxid TAXID
</code></pre>
<p>where GENOME.fa is the input fasta file with the genome, and TAXID is the
NCBI taxonomy ID for the species associated with the genome.
TaxIDs can be found using the NCBI taxonomy website
(<a href="https://www.ncbi.nlm.nih.gov/taxonomy" rel="nofollow">https://www.ncbi.nlm.nih.gov/taxonomy</a>).</p>
<p>After this, create a .nal file using:</p>
<pre><code>blastdb_aliastool -dblist "GENOME_db" \
-dbtype nucl -out GENOME_db -title "GENOME"
</code></pre>
<p>The blastDbSetup.sh script can be used to automate these steps. It can
be run with:</p>
<pre><code>bash /path/to/pipeline/setupBlastDb/blastDbSetup.sh GENOME.fa TAXON_ID
</code></pre>
<ol start="2">
<li>Full database creation:</li>
</ol>
<p>Once you've created all your sub-databases (e.g. GENOME1, GENOME2,
GENOME3, ..., GENOME_N), create a .nal file to represent the full
database using:</p>
<pre><code>blastdb_aliastool -dblist "GENOME1_db GENOME2_db GENOME3_db ... GENOME_N_db" \
-dbtype nucl -out contaminant_db -title "Contaminant Database"
</code></pre>
<p>If, at a later time, you need to change your contaminant database, you
then only need to rebuild the modified portion, and then update this
file to reflect that.</p>
<h2>
<a id="user-content-6-bed-file-preparation" class="anchor" href="#6-bed-file-preparation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>6: Bed file preparation</h2>
<p>A bed file is a file which details regions of the genome in which you
are interested. The syntax for bed files is described at
<a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1" rel="nofollow">https://genome.ucsc.edu/FAQ/FAQformat.html#format1</a>.</p>
<p>If you know which genes you are targeting and are using a common
published genome, the target bed file can be downloaded from the UCSC Table
Browser (<a href="https://genome.ucsc.edu/cgi-bin/hgTables" rel="nofollow">https://genome.ucsc.edu/cgi-bin/hgTables</a>). Otherwise, it can
be created using results from a BLAST search or any other method you
like. <strong>This pipeline does not currently support overlapping intervals, but
does support blocks as described in the bed spec.</strong></p>
<p>This pipeline can also optionally use a masking bed file, for if there are
genomic regions where you know there will be a high number of artifactual
variants, or which you would like to ignore for other reasons. The masking bed
file only needs to contain the first three bed columns (chrom, start, and stop),
and will ignore any other columns provided.</p>
<h2>
<a id="user-content-7-configuration-file-creation" class="anchor" href="#7-configuration-file-creation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>7: Configuration file creation:</h2>
<p>Use the ConfigTemplate to create a new file with the appropriate headers.
For each row, fill in the information about a particular sample. Note that in
most cases, "path" refers to an absolute path, with the exception of "in1" and
"in2", where you just need the name of the input file. The "blast_db" option
is the path to the appropriate .nal or .nhr file, minus the .nal or .nhr
extension, but can also be specified as "none" to skip BLAST filtering.</p>
<table>
<thead>
<tr>
<th>Header</th>
<th>Required or Default</th>
<th>Information</th>
</tr>
</thead>
<tbody>
<tr>
<td>sample</td>
<td>Required</td>
<td>A unique identifier for a sample; this will be used to name all output files for this sample</td>
</tr>
<tr>
<td>rglb</td>
<td>Required</td>
<td>Read Group Library Identifier</td>
</tr>
<tr>
<td>rgpl</td>
<td>Required</td>
<td>Read Group Platform; usually Illumina</td>
</tr>
<tr>
<td>rgpu</td>
<td>Required</td>
<td>Read Group Platform Unit</td>
</tr>
<tr>
<td>rgsm</td>
<td>Required</td>
<td>Read Group Sample</td>
</tr>
<tr>
<td>reference</td>
<td>Required</td>
<td>The path to the prepared reference genome to use with this sample.</td>
</tr>
<tr>
<td>target_bed</td>
<td>Required</td>
<td>A bed file showing where the targets are for this particular sample</td>
</tr>
<tr>
<td>maskBed</td>
<td>NONE</td>
<td>A bed file to use for masking variants.</td>
</tr>
<tr>
<td>blast_db</td>
<td>NONE</td>
<td>The blast database to use for contaminant filtering; must include your target genome, if used.</td>
</tr>
<tr>
<td>targetTaxonId</td>
<td>9606</td>
<td>The taxon ID of the species you are expecting to be present in the sample.</td>
</tr>
<tr>
<td>baseDir</td>
<td>Required</td>
<td>The directory the input files are in, and where the output files will be created.</td>
</tr>
<tr>
<td>in1</td>
<td>Required</td>
<td>The read1 fastq (or fastq.gz, or fq.gz, or fq) file for this sample. Note that this is just the name of the file, and not the full path.</td>
</tr>
<tr>
<td>in2</td>
<td>Required</td>
<td>The read2 fastq (or fastq.gz, or fq.gz, or fq) file for this sample. Note that this is just the name of the file, and not the full path.</td>
</tr>
<tr>
<td>mqFilt</td>
<td>0</td>
<td>A threshold for mapping quality filtering, if desired.</td>
</tr>
<tr>
<td>minMem</td>
<td>0</td>
<td>The minimum number of reads that must be in a family for consensus making</td>
</tr>
<tr>
<td>maxMem</td>
<td>200</td>
<td>The maximum number of reads in a family the consensus maker should consider.</td>
</tr>
<tr>
<td>cutOff</td>
<td>0.9</td>
<td>The threshold for consensus making; the consensus maker will require at least this much agreement on a per base pair level.</td>
</tr>
<tr>
<td>nCutOff</td>
<td>1</td>
<td>The maximum proportion of N bases in an output consensus sequence.</td>
</tr>
<tr>
<td>umiLen</td>
<td>8</td>
<td>The length of the UMI in this sample</td>
</tr>
<tr>
<td>spacerLen</td>
<td>1</td>
<td>The length of the spacer sequence in this sample</td>
</tr>
<tr>
<td>locLen</td>
<td>10</td>
<td>The localization length to use for this sample</td>
</tr>
<tr>
<td>readLen</td>
<td>101</td>
<td>The length of a read for this sample</td>
</tr>
<tr>
<td>adapterSeq</td>
<td>"ANNNNNNNNAGATCGGAAGAG"</td>
<td>The adapter sequence used in library preperation, with UMI bases as Ns, and spacer sequence included. Alternatively, a fasta file with all possible UMI-adapter conbinations. Used by cutadapt for adapter clipping.</td>
</tr>
<tr>
<td>clipBegin</td>
<td>7</td>
<td>How many bases to clip off the 5' end of the read</td>
</tr>
<tr>
<td>clipEnd</td>
<td>0</td>
<td>How many bases to clip off the 3' end of the read</td>
</tr>
<tr>
<td>minClonal</td>
<td>0</td>
<td>The minimum clonality to use for count_muts generation</td>
</tr>
<tr>
<td>maxClonal</td>
<td>0.1</td>
<td>The maximum clonality to use for count_muts generation</td>
</tr>
<tr>
<td>minDepth</td>
<td>100</td>
<td>The minimum depth to use for count_muts generation</td>
</tr>
<tr>
<td>maxNs</td>
<td>1</td>
<td>The maximum proportion of N bases to use for count_muts generation</td>
</tr>
<tr>
<td>recovery</td>
<td>"noRecovery.sh"</td>
<td>The recovery script to use in attempting to recover ambiguously mapped reads (as determine by blast alignment vs bwa alignment). Recovery script creation is discussed in 8; below.</td>
</tr>
<tr>
<td>cluster_dist</td>
<td>10</td>
<td>How close together variants have to be to be considered 'clustered'</td>
</tr>
<tr>
<td>cm_outputs</td>
<td>"GB"</td>
<td>Select which sections of the countmuts to output, in addition to 'OVERALL'. String of one or more of 'G', 'B', and 'N'. G -> output GENE sections for each bed line; B -> output 'BLOCK' sections for each block in the bed line (if present); 'N' -> Only output overall frequencies. Overrides all other options.</td>
</tr>
<tr>
<td>cm_sumTypes</td>
<td>"GT"</td>
<td>How to calculate OVERALL and GENE blocks for countmuts output. The first character controls summing for overall: G -> OVERALL = sum(GENEs); B -> OVERALL = sum(BLOCKs). In sum(GENEs) mode, this will ignore BLOCKs for the purposes of calculating OVERALL. The second character controls summing for each GENE: T -> GENE = Whole gene, ignoring BLOCKs; B -> GENE = sum(BLOCKs).</td>
</tr>
<tr>
<td>cm_filters</td>
<td>"none"</td>
<td>Select which filters to apply during frequency calculation. These filters will also be applied during muts_per_cycle calculation. Available filters are: SNP, near_indel, clustered, masked, low_depth.</td>
</tr>
<tr>
<td>runSSCS</td>
<td>false</td>
<td>true or false; whether to do full analysis for SSCS data.</td>
</tr>
<tr>
<td>rerun_type</td>
<td>0 (Required for rerun)</td>
<td>What type of rerun you want to do. 0 -> no rerun; 1 -> rerun variant caller; 2 -> rerun postBlastRecovery; 3 -> rerun BLAST and alignment; 4 -> rerun consensus maker.</td>
</tr>
</tbody>
</table>
<p>Save the file as a .csv file with unix line endings (LF).</p>
<h2>
<a id="user-content-8-recovery-script-creation" class="anchor" href="#8-recovery-script-creation" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>8: Recovery script creation</h2>
<p>As part of its operation, this pipeline filters out correct-species reads
where the blast mapping and bwa mapping positions disagree or where blast
is unable to determine conclusively where the read maps (i.e.E-scores are
the same). There is a step which provides an option to recover those reads
by using a user-generated bash script. Currently, we use a bash script to
call a python script which will actually accomplish the recovery, but this
functionality may be changed in the future. In general, these scripts must:</p>
<ol>
<li>accept ambiguous reads as $1</li>
<li>accept non-ambiguous reads as $2</li>
<li>accept reads labeled as incorrect species as $3</li>
<li>take a name base for output files as $4</li>
<li>take a basePath for location of script files as $5</li>
</ol>
<p>The script must create the following output files:</p>
<ul>
<li>${4}.recovered.temp.bam</li>
<li>${4}.ambig.bam</li>
<li>${4}.wrongSpecies.bam</li>
</ul>
<p>All script files must be stored in scripts/RecoveryScripts.</p>
<p>Any packages required by your recovery script can be added to the envs/DS_env_recovery.yaml file. By default, this contains the conda packages (from bioconda or conda-forge):</p>
<ul>
<li>Python 3.6</li>
<li>samtools</li>
<li>pysam</li>
<li>snakemake</li>
<li>pandas</li>
<li>regex</li>
<li>biopython</li>
<li>pandoc</li>
</ul>
<p>Note that if you decide to write your own recovery scripts, you are
responsible for ensuring that your recovery scripts actually work as
intended, and do not break your computer. We are unable to guarantee
that any sample run with a recovery script other than one of the ones
provided with the pipeline will produce accurate data.</p>
<h2>
<a id="user-content-9-running-pipelines" class="anchor" href="#9-running-pipelines" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>9: Running pipelines:</h2>
<p>The pipeline can be run using the DS command created by the setup script:</p>
<div class="highlight highlight-source-shell"><pre>/path/to/Duplex-Seq-Pipeline/DS CONFIG_CSV.csv</pre></div>
<h2>
<a id="user-content-10-output-file-descriptions" class="anchor" href="#10-output-file-descriptions" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>10: Output file descriptions:</h2>
<p>The pipeline will create a set of summary files covering all samples, as
well as a file directory structure for each sample. The summary files are:</p>
<table>
<thead>
<tr>
<th>File Name</th>
<th>Description</th>
</tr>
</thead>
<tbody>
<tr>
<td>summary.csv</td>
<td>A csv file with summary metrics for all samples.</td>
</tr>
<tr>
<td>summaryDepth.pdf</td>
<td>A pdf file containing depth per target plots for all samples.</td>
</tr>
<tr>
<td>summaryFamilySize.pdf</td>
<td>A pdf file containing family size plots for all samples.</td>
</tr>
<tr>
<td>summaryInsertSize.pdf</td>
<td>A pdf file containing insert size plots for all samples.</td>
</tr>
<tr>
<td>summaryMutsByCycle.pdf</td>
<td>A pdf file containing non-SNP mutations per cycle for all samples.</td>
</tr>
</tbody>
</table>
<p>This directory structure after a run looks like this:</p>
<div class="highlight highlight-source-shell"><pre><span class="pl-c1">.</span>
└──SAMP_DIR
├── Final
│ ├── dcs
│ │ ├── FilteredReads
│ │ │ ├── SAMPLE_dcs.postRecovery.ambig.bam
│ │ │ ├── SAMPLE_dcs.postRecovery.ambig.bam.bai
│ │ │ ├── SAMPLE_dcs.postRecovery.wrongSpecies.bam
│ │ │ └── SAMPLE_dcs.postRecovery.wrongSpecies.bam.bai
│ │ ├── SAMPLE.dcs.countmuts.csv
│ │ ├── SAMPLE.dcs.final.bam
│ │ ├── SAMPLE.dcs.final.bam.bai
│ │ ├── SAMPLE.dcs.mutated.bam
│ │ ├── SAMPLE.dcs.mutated.bam.bai
│ │ ├── SAMPLE.dcs.snps.vcf
│ │ └── SAMPLE.dcs.vcf
│ ├── SAMPLE.report.html
│ └── sscs
│ ├── SAMPLE.sscs.countmuts.csv
│ ├── SAMPLE.sscs.final.bam
│ ├── SAMPLE.sscs.final.bam.bai
│ ├── SAMPLE.sscs.mutated.bam
│ ├── SAMPLE.sscs.mutated.bam.bai
│ ├── SAMPLE.sscs.snps.vcf
│ └── SAMPLE.sscs.vcf
├── Intermediate
│ ├── ConsensusMakerOutputs
│ │ ├── SAMPLE_aln_seq1.fq.gz
│ │ ├── SAMPLE_aln_seq2.fq.gz
│ │ ├── SAMPLE_read1_dcs.fq.gz
│ │ ├── SAMPLE_read1_sscs.fq.gz
│ │ ├── SAMPLE_read2_dcs.fq.gz
│ │ └── SAMPLE_read2_sscs.fq.gz
│ ├── preVariantCalling
│ │ ├── SAMPLE.dcs.prevar.bam
│ │ └── SAMPLE.sscs.prevar.bam
│ └── postBlast
│ ├── FilteredReads
│ │ ├── SAMPLE_dcs.ambig.sort.bam
│ │ ├── SAMPLE_dcs.ambig.sort.bam.bai
│ │ ├── SAMPLE_dcs.wrongSpecies.sort.bam
│ │ └── SAMPLE_dcs.wrongSpecies.sort.bam.bai
│ ├── SAMPLE_dcs.blast.xml
│ ├── SAMPLE_dcs.preBlast.mutated.bam
│ └── SAMPLE_dcs.preBlast.unmutated.bam
├── logs
│ └── Log files
├── testSeq1.fastq.gz
├── testSeq2.fastq.gz
└── Stats
├── data
│ ├── SAMPLE_cmStats.txt
│ ├── SAMPLE.dcs_ambiguity_counts.txt
│ ├── SAMPLE.dcs.iSize_Metrics.txt
│ ├── SAMPLE.dcs_MutsPerCycle.dat.csv
│ ├── SAMPLE.dcs.mutsPerRead.txt
│ ├── SAMPLE.sscs_MutsPerCycle.dat.csv
│ ├── SAMPLE.sscs.mutsPerRead.txt
│ ├── SAMPLE.dcs.depth.txt
│ ├── SAMPLE.dcs.depth.summary.csv
│ ├── SAMPLE.sscs.depth.txt
│ ├── SAMPLE.sscs.depth.summary.csv
│ ├── SAMPLE_dcs.speciesComp.txt
│ ├── SAMPLE_mem.dcs.sort.flagstats.txt
│ ├── SAMPLE_mem.sscs.sort.flagstats.txt
│ ├── SAMPLE.dcs.endClip.metrics.txt
│ ├── SAMPLE.dcs.overlapClip.metrics.txt
│ ├── SAMPLE.sscs.endClip.metrics.txt
│ ├── SAMPLE.sscs.overlapClip.metrics.txt
│ ├── SAMPLE_onTargetCount.txt
│ ├── SAMPLE.sscs_onTargetCount.txt
│ ├── SAMPLE.dcs_onTargetCount.txt
│ ├── SAMPLE.tagstats.txt
│ └── SAMPLE.temp.sort.flagstats.txt
├── SAMPLE.report.ipynb
└── plots
├── SAMPLE.dcs.iSize_Histogram.png
├── SAMPLE.dcs.mutsPerRead.png
├── SAMPLE.dcs.targetCoverage.png
├── SAMPLE.dcs_BasePerPosInclNs.png
├── SAMPLE.dcs_BasePerPosWithoutNs.png
├── SAMPLE.sscs.mutsPerRead.png
├── SAMPLE.sscs_BasePerPosInclNs.png
├── SAMPLE.sscs_BasePerPosWithoutNs.png
├── SAMPLE_fam_size_relation.png
└── SAMPLE_family_size.png</pre></div>
<p>File descriptions are as follows:</p>
<table>
<thead>
<tr>
<th>Directory</th>
<th>File name</th>
<th>Description</th>
<th>When Generated</th>
</tr>
</thead>
<tbody>
<tr>
<td>SAMP_DIR</td>
<td>SAMPLE_seq1.fastq.gz</td>
<td>Input read 1 file</td>
<td>Input</td>
</tr>
<tr>
<td>SAMP_DIR</td>
<td>SAMPLE_seq2.fastq.gz</td>
<td>Input read 2 file</td>
<td>Input</td>
</tr>
<tr>
<td>SAMP_DIR</td>
<td>Final</td>
<td>Directory containing final bam and vcf files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final</td>
<td>dcs</td>
<td>Directory containing final dcs files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>FilteredReads</td>
<td>Directory containing reads still filtered after postBlastRecovery</td>
<td>blast_db!=NONE</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs/FilteredReads</td>
<td>SAMPLE.dcs.postRecovery.ambig.bam</td>
<td>File containing reads still considered ambiguous after postBlastRecovery. May be empty.</td>
<td>blast_db!=NONE</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs/FilteredReads</td>
<td>SAMPLE.dcs.postRecovery.ambig.bam.bai</td>
<td>Index for SAMPLE.dcs.postRecovery.ambig.bam</td>
<td>blast_db!=NONE</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs/FilteredReads</td>
<td>SAMPLE.dcs.postRecovery.wrongSpecies.bam</td>
<td>File containing reads still considered ambiguous after postBlastRecovery. May be empty.</td>
<td>blast_db!=NONE</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs/FilteredReads</td>
<td>SAMPLE.dcs.postRecovery.wrongSpecies.bam.bai</td>
<td>Index for SAMPLE.dcs.postRecovery.wrongSpecies.bam</td>
<td>blast_db!=NONE</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.countmuts.csv</td>
<td>Countmuts file, showing a summary of mutation data for DCS reads.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.final.bam</td>
<td>Final file for DCS reads, including all reads that overlap the bed file.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.final.bam.bai</td>
<td>Index for final DCS reads.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.mutated.bam</td>
<td>File containing DCS reads with non-SNP mutations</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.mutated.bam.bai</td>
<td>Index for DCS mutated reads file.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.snps.vcf</td>
<td>VCF file containing SNPs overlapping bed file in DCS.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/dcs</td>
<td>SAMPLE.dcs.vcf</td>
<td>VCF file containing all variants overlapping bed file in DCS.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final</td>
<td>SAMPLE.report.html</td>
<td>Summary report for this sample</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final</td>
<td>sscs</td>
<td>Directory containing final SSCS files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.countmuts.csv</td>
<td>Countmuts file, showing a summary of mutation data for SSCS reads.</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.final.bam</td>
<td>Final file for SSCS reads, including all reads that overlap the bed file.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.final.bam.bai</td>
<td>Index for final SSCS reads.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.mutated.bam</td>
<td>File containing SSCS reads with non-SNP mutations</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.mutated.bam.bai</td>
<td>Index for SSCS mutated reads file.</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.snps.vcf</td>
<td>VCF file containing SNPs overlapping bed file in SSCS.</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Final/sscs</td>
<td>SAMPLE.sscs.vcf</td>
<td>VCF file containing all variants overlapping bed file in SSCS.</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR</td>
<td>Intermediate</td>
<td>Directory containing intermediate checkpointing files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate</td>
<td>ConsensusMakerOutputs</td>
<td>Directory for post-consensus maker checkpoint files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_aln_seq1.fq.gz</td>
<td>Read 1 file for raw on-target determination</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_aln_seq2.fq.gz</td>
<td>Read 2 file for raw on-target determination</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_read1_dcs.fq.gz</td>
<td>DCS Read 1 File</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_read1_sscs.fq.gz</td>
<td>SSCS Read 1 file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_read2_dcs.fq.gz</td>
<td>DCS Read 2 File</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/ConsensusMakerOutputs</td>
<td>SAMPLE_read2_sscs.fq.gz</td>
<td>SSCS Read 2 file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate</td>
<td>preVariantCalling</td>
<td>Directory for pre-variant calling checkpoint files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/preVariantCalling</td>
<td>SAMPLE.dcs.prevar.bam</td>
<td>DCS pre-variant file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/preVariantCalling</td>
<td>SAMPLE.sscs.prevar.bam</td>
<td>SSCS pre-variant file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/</td>
<td>postBlast</td>
<td>Directory for post-BLAST checkpoint files. Only affects DCS.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast</td>
<td>FilteredReads</td>
<td>Directory for reads that got filtered out of DCS processing due to BLAST analysis indicating that they were either the wrong species or ambiguously mapped.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast/FilteredReads</td>
<td>SAMPLE_dcs.ambig.sort.bam</td>
<td>Reads that were filtered out due to ambiguous mapping according to BLAST alignment.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast/FilteredReads</td>
<td>SAMPLE_dcs.ambig.sort.bam.bai</td>
<td>Index for ambiguous reads file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast/FilteredReads</td>
<td>SAMPLE_dcs.wrongSpecies.sort.bam</td>
<td>Reads that were filtered out due to BLAST alignment indicating that they were from the wrong species, or where species of origin could not be determined.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast/FilteredReads</td>
<td>SAMPLE_dcs.wrongSpecies.sort.bam.bai</td>
<td>Index for wrong-species file</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast</td>
<td>SAMPLE_dcs.blast.xml</td>
<td>BLAST xml output</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast</td>
<td>SAMPLE_dcs.preBlast.mutated.bam</td>
<td>DCS with potential non-SNP variants that were submitted to BLAST.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Intermediate/postBlast</td>
<td>SAMPLE_dcs.preBlast.unmutated.bam</td>
<td>DCS reads without non-SNP variants.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR</td>
<td>logs</td>
<td>Directory containing log files for this sample. Log files are currently empty, but will be filled later.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR</td>
<td>Stats</td>
<td>Directory containing statistics files</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats</td>
<td>data</td>
<td>Directory containing statistics data files.</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE_cmStats.txt</td>
<td>Statistics from the Consensus Maker</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs_ambiguity_counts.txt</td>
<td>Statistics on ambiguity counts</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs.iSize_Metrics.txt</td>
<td>Statistics on insert size in DCS</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs_MutsPerCycle.dat.csv</td>
<td>Statistics file for non-SNP mutations per cycle in DCS reads</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs.mutsPerRead.txt</td>
<td>Statistics file for non-SNP mutations per read in DCS reads</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.sscs_MutsPerCycle.dat.csv</td>
<td>Text data of error rate per cycle in unclipped SSCS</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.sscs.mutsPerRead.txt</td>
<td>Statistics file for non-SNP mutations per read in SSCS reads</td>
<td>runSscs=True</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs.depth.txt</td>
<td>Per-base coverage and N counts for final DCS</td>
<td>Always</td>
</tr>
<tr>
<td>SAMP_DIR/Stats/data</td>
<td>SAMPLE.dcs.depth.summary.csv</td>
<td>Per-bed region min, mean, median, and max non-zero depth for final DCS.</td>
<td>Always</td>
</tr>
<tr>