Command Line Interface¶

To access the help menu:

$ sam2lca --help

The list of arguments of options is detailed below

sam2lca¶

sam2lca: Lowest Common Ancestor on SAM/BAM/CRAM alignment files
Author: Maxime Borry, Alexander Huebner
Contact: <maxime_borry[at]eva.mpg.de>
Homepage & Documentation: github.com/maxibor/sam2lca

sam2lca [OPTIONS] COMMAND [ARGS]...

Options

--version¶: Show the version and exit.

-d, --dbdir <dbdir>¶

Directory to store taxonomy databases

Default: /home/docs/.sam2lca

analyze¶

Run the sam2lca analysis

SAM: path to SAM/BAM/CRAM alignment file

sam2lca analyze [OPTIONS] SAM

Options

-t, --taxonomy <taxonomy>¶

Taxonomy database to use

Default: ncbi

-a, --acc2tax <acc2tax>¶

acc2tax database to use

Default: nucl

-i, --identity <identity>¶

Minimum identity threshold NOTE: This argument is mutually exclusive with arguments: [distance].

Default: 0.8

-d, --distance <distance>¶: Edit distance threshold NOTE: This argument is mutually exclusive with arguments: [identity].

-l, --length <length>¶

Minimum alignment length

Default: 30

-c, --conserved¶: Ignore reads mapping in ultraconserved regions

-p, --process <process>¶

Number of process for parallelization

Default: 2

-o, --output <output>¶: sam2lca output file. Default: [basename].sam2lca.*

-b, --bam_out¶: Write BAM output file with XT tag for TAXID

-r, --bam_split_rank <bam_split_rank>¶

Write BAM output file split by TAXID at rank -r. To use in combination with -b/–bam_out

Options: strain|species|genus|family|order|class|phylum|superkingdom

-n, --bam_split_read <bam_split_read>¶

Minimum numbers of reads to write BAM split by TAXID. To use in combination with -b/–bam_out

Default: 50

Arguments

SAM¶: Required argument

list-db¶

List available taxonomy and acc2tax databases

sam2lca list-db [OPTIONS]

update-db¶

Download/prepare acc2tax and taxonomy databases

sam2lca update-db [OPTIONS]

Options

-t, --taxonomy <taxonomy>¶

Name of taxonomy database to create (ncbi | gtdb)

Default: ncbi

--taxo_names <taxo_names>¶: names.dmp file for Taxonomy database (optional). Only needed for custom taxonomy database (non ncbi or gtdb)

--taxo_nodes <taxo_nodes>¶: nodes.dmp file for Taxonomy database (optional). Only needed for custom taxonomy database (non ncbi or gtdb)

--taxo_merged <taxo_merged>¶: merged.dmp file for Taxonomy database (optional). Only needed for custom taxonomy database (non ncbi or gtdb)

-a, --acc2tax <acc2tax>¶: Type of acc2tax mapping database to build.

--acc2tax_json <acc2tax_json>¶

JSON file for specifying extra acc2tax mappings

Default: https://raw.githubusercontent.com/maxibor/sam2lca/master/data/acc2tax.json