Command Line Interface¶
To access the help menu:
$ sam2lca --help
The list of arguments of options is detailed below
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¶
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
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