User manual

Configuration description

1. Ancient data input as reads:

This section is specific to the configuration of processing sequencing reads from ancient (meta)genomic samples.

• input_type <string> [optional]:   The type of genomic information. Default: "reads".
  
• reference_genome <string> [required]   The reference genome representative of a microbial species, in FASTA format. This parameter is equivalent to --reference in the --help menu.
  
• age_type <int> [optional]:   Age type of sample ( 1 indicates ancient type and 2 indicates contemporary type) . Default: 1.
  

* `intermediate` `` `[optional]`:   The directory for storing intermediate files. Default: "intermediates" in current directory. This parameter is equivalent to `--intermediate_dir` in the `--help` menu.

* `search_report_mode` `<"-k,int">` `[optional]`:   The upper limit on the number of alignments Bowtie 2 should report in the search of alignments. Default: "-k,5". (The higher the value is set the more computational time required , but more accurate alignment returned.)

* `bowtie2_threads` `` `[optional]`:   The thread number for bowtie2 to process each sample. Default: [1].

* `minimum_mapping_quality` `` `[optional]`:   Bases with quality score lower than the specified value will be ignored in reconstructing genome alignment. Default: [30].

* `minimum_mapping_length` `` `[optional]`:   Aligned reads with length shorter than the specified value will be ignored in reconstructing genome alignment. Default: [30].

* `maximum_snp_edit_distance` `` `[optional]`:   Reads with SNP edit distance greater than the specified value will be ignored in reconstructing genome alignment. Default: [0.03].

* `nproc` `` `[optional]`:   The number of processors for handling multiple samples in parallel. Default: [1].

* `minimum_coverage` `` `[optional]`:   A position with a coverage depth lower than the specified value will be ignored in reconstructing genome alignment. Default: [5].

* `trim_distance` `<"int:int">` `[optional]`:   The number of nucleotides to trim at two ends of ancient reads. These positions are likely post-mortem damages. Default: "5:5".

* `dominant_allele_frequency` `` `[optional]`:   A position with the degree of dominant allele lower than the specified value will be ignored in reconstructing genome alignment. Default: [0.8].

* `output_trimmed_reads` `` `[optional]`: Specify 1 if you need to output aligned trimmed reads which are used in reconstructing genome alignment; Specify 0 if you want to skip this feature. Default: [0].

* `sample` `` `[required]`: The directory holding ancient metagenomics reads folders. This parameter is equivalent to `--ancient_metagenomes` in the `--help` menu.

2. Modern data input as reads:

This section is specific to the configuration of processing sequencing reads from modern (meta)genomic samples.

• input_type <string> [optional]:   The type of genomic information. Default: "reads".
  

* `reference_genome` `` `[required]`   The reference genome representative of a microbial species, in FASTA format. This parameter is equivalent to `--reference` in the `--help` menu.

* `age_type` `` `[optional]`:   Age type of sample ( 1 indicates ancient type and 2 indicates contemporary type) . Default: 2.

* `intermediate` `` `[optional]`:   The directory for storing intermediate files. Default: "intermediates" in current directory. This parameter is equivalent to `--intermediate_dir` in the `--help` menu.

* `search_report_mode` `<"-k,int">` `[optional]`:   The upper limit on the number of alignments Bowtie 2 should report in the search of alignments. Default: "-k,5". (The higher the value is set the more computational time required , but more accurate alignment returned.)

* `bowtie2_threads` `` `[optional]`:   The thread number for bowtie2 to process each sample. Default: [1].

* `minimum_mapping_quality` `` `[optional]`:   Bases with quality score lower than the specified value will be ignored in reconstructing genome alignment. Default: [30].

* `minimum_mapping_length` `` `[optional]`:   Aligned reads with length shorter than the specified value will be ignored in reconstructing genome alignment. Default: [30].

* `maximum_snp_edit_distance` `` `[optional]`:   Reads with SNP edit distance greater than the specified value will be ignored in reconstructing genome alignment. Default: [0.03].

* `nproc` `` `[optional]`:   The number of processors for handling multiple samples in parallel. Default: [1].

* `minimum_coverage` `` `[optional]`:   A position with a coverage depth lower than the specified value will be ignored in reconstructing genome alignment. Default: [5].

* `trim_distance` `<"int:int">` `[optional]`:   The number of nucleotides to trim at two ends of ancient reads. These positions are likely post-mortem damages. Default: "5:5".

* `dominant_allele_frequency` `` `[optional]`:   A position with the degree of dominant allele lower than the specified value will be ignored in reconstructing genome alignment. Default: [0.8].

• sample <string> [required]: The directory holding modern metagenomics reads folders. This parameter is equivalent to --modern_metagenomes in the --help menu.
  

3. Assembled genomes input as contigs:

This section is specific to the configuration of processing assembled genomes as input.

• input_type <string> [optional]:   The type of genomic information. Default: "contigs".
  

* `reference_genome` `` `[required]`:   The reference genome representative of a microbial species, in FASTA format. This parameter is equivalent to `--reference` in the `--help` menu.

* `intermediate` `` `[optional]`:   directory for storing intermediate files. Default: "". This parameter is equivalent to `--intermediate_dir` in the `--help` menu.

* `homolog_length` `` `[optional]`:   The minimum length for the aligned part of a contig to be considered as a homolog in order to be used in reconstructing genome alignment. Default: [500].

* `homolog_identity` `` `[optional]`:   The minimum identity for the aligned part of a contig to be considered as a homolog in order to be used in reconstructing genome alignment. Default: [95.0]

* `blastn_threads` `` `[optional]`:   Specify the number of threads used for blastn. Note: please use < 8 CPUs if you are using blastn >2.7.0

* `sample` `` `[required]`: Specify the directory holding assembled contigs files. Default: "". This parameter is equivalent to `--genome_assemblies` in the `--help` menu.