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updating README.md (abismal capitalization and user flags)
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guilhermesena1 committed Aug 3, 2021
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## ABISMAL ##
## abismal ##

**A**nother **Bis**ulfite **M**apping **Al**gorithm (ABISMAL) is
**A**nother **Bis**ulfite **M**apping **Al**gorithm (abismal) is
a read mapping program for bisulfite sequencing in DNA methylation
studies.

### Requirements ###

Currently ABISMAL requires a C++ compiler that supports the C++11
Currently abismal requires a C++ compiler that supports the C++11
standard and OpenMP. The default compiler assumed is g++ (comes with
GCC, available on your Linux or OS X machine). The g++ compiler has
supported the C++11 standard since roughly 2012 (GCC 4.7) so this
should not cause any problems. It also requires an OMP library and
headers to be available, which rarely causes problems. ABISMAL also is
headers to be available, which rarely causes problems. abismal also is
capable of reading input files (FASTQ format) that are gzip
compressed. This requires that the ZLib library is installed on the
system; this is also rarely a problem.

If you have trouble with the `make` part of the installation procedure
described below, please contact me.
described below, please contact us via e-mail or through a [GitHub
issue](https://github.com/smithlabcode/abismal/issues).

### Installation from a clone of the repo ###

Expand Down Expand Up @@ -68,25 +69,26 @@ paired-end reads
$ abismal [options] -i <index-file> -o <output-file> <read_1.fq> <read_2.fq>
```

### ABISMAL Options ###

|option|long version |arg type |default|description |
|:-----|:------------|:--------|------:|:--------------------------------------------------|
| -i | -index | string | | genome index file [required] |
| -o | -outfile | string | stdout | output SAM file |
| -t | -threads | integer | 1 | number of mapping threads |
| -b | -batch | integer | 20,000 | number of reads to load at once |
| -c | -candidates | integer | 0 (automatic) | maximum candidates for comparison |
| -p | -max-mates | integer | 20 | max number of candidates for mating |
| -l | -min-frag | integer | 32 | minimum fragment length (PE mode) |
| -L | -max-frag | integer | 3,000 | maximum fragment length (PE mode) |
| -M | -max-error | double | 0.1 | max relative number of errors |
| -s | -mapstats | string | | mapping statistics output file |
| -a | -ambig | | | report a position for ambiguous reads |
| -P | -pbat | | | input follows the PBAT protocol |
| -R | -random-pbat| | | input follows the random PBAT protocol|
| -A | -a-rich | | | reads are A-rich (SE mode) |
| -V | -verbose | | | print more run info |
### abismal options ###

|option|long version |arg type |default |description |
|:-----|:--------------|:--------|------------------:|:--------------------------------------|
| -i | -index | string | | genome index file |
| -g | -genome | string | | genome file (FASTA) |
| -o | -outfile | string | stdout | output file (SAM) |
| -t | -threads | integer | 1 | number of mapping threads |
| -b | -batch | integer | 20,000 | number of reads to load at once |
| -c | -candidates | integer | 0 (automatic) | maximum candidates for comparison |
| -p | -max-mates | integer | 20 | max number of candidates for mating |
| -l | -min-frag | integer | 32 | minimum fragment length (PE mode) |
| -L | -max-frag | integer | 3,000 | maximum fragment length (PE mode) |
| -m | -max-distance | double | 0.1 | max relative number of errors |
| -s | -stats | string | | mapping statistics output file (YAML) |
| -a | -ambig | | | report a position for ambiguous reads |
| -P | -pbat | | | input follows the PBAT protocol |
| -R | -random-pbat | | | input follows the random PBAT protocol|
| -A | -a-rich | | | reads are A-rich (SE mode) |
| -V | -verbose | | | print more run info |

### Examples ###

Expand Down Expand Up @@ -120,14 +122,16 @@ $ abismal -g hg38.fa -o reads.sam reads.fq
Mapping results are reported in SAM format. Some choices in the output
are explicitly highlighted below:
* Reads are output identically to how they were read, regardless of
mapped strand
mapped strand.
* the `NM` tag reports the edit distance between the read and the
output, specifically the sum of mismatches, insertions and
deletions to the best mapping position.
* The `CV` tag reports the assumed bisulfite base used to map the
read. Reads mapped as A-rich will be reported with `CV:A:A`, and
reads mapped as T-rich will be reported with `CV:A:T`. This tag is
independent of the strand the read was mapped to.
independent of the strand the read was mapped to. If reads are not
mapped in PBAT or random PBAT mode, the first end will always be
T-rich and the second end will always be A-rich.

### Contacts ###

Expand All @@ -140,12 +144,12 @@ Copyright (C) 2018-2021 Andrew D. Smith and Guilherme de Sena Brandine

Authors: Andrew D. Smith and Guilherme de Sena Brandine

ABISMAL is free software: you can redistribute it and/or modify it under
abismal is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free
Software Foundation, either version 3 of the License, or (at your
option) any later version.

ABISMAL is distributed in the hope that it will be useful, but WITHOUT
abismal is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
for more details.

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