NAME
coverm make - Generate BAM files through mapping (version: 0.5.0)
SYNOPSIS
coverm make <REFERENCE> <READ_DEFINITION> <OUTPUT> ..
DESCRIPTION
coverm make generates BAM files by read mapping a set of reads against a reference FASTA database.
READ MAPPING PARAMETERS
- -1 PATH ..
Forward FASTA/Q file(s) for mapping. These may be gzipped or not.
- -2 PATH ..
Reverse FASTA/Q file(s) for mapping. These may be gzipped or not.
- -c, --coupled PATH ..
One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order <sample1_R1.fq.gz> <sample1_R2.fq.gz> <sample2_R1.fq.gz> <sample2_R2.fq.gz> ..
- --interleaved PATH ..
Interleaved FASTA/Q files(s) for mapping. These may be gzipped or not.
- --single PATH ..
Unpaired FASTA/Q files(s) for mapping. These may be gzipped or not.
REFERENCE
- -r, --reference PATH
FASTA file of contigs e.g. concatenated genomes or metagenome assembly, or minimap2 index (with
--minimap2-reference-is-index), or BWA index stem (with-p bwa-mem). [required]
MAPPING ALGORITHM OPTIONS
-p, --mapper NAME
| name | description |
|---|---|
minimap2-sr |
minimap2 with '-x sr' option |
bwa-mem |
bwa mem using default parameters |
minimap2-ont |
minimap2 with '-x map-ont' option |
minimap2-pb |
minimap2 with '-x map-pb' option |
minimap2-no-preset |
minimap2 with no '-x' option |
- --minimap2-params PARAMS
Extra parameters to provide to minimap2, both indexing command (if used) and for mapping. Note that usage of this parameter has security implications if untrusted input is specified. '
-a' is always specified to minimap2. [default: none]
- --minimap2-reference-is-index
Treat reference as a minimap2 database, not as a FASTA file. [default: not set]
- --bwa-params PARAMS
Extra parameters to provide to BWA. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]
OUTPUT
- -o, --output-directory DIR
Where generated BAM files will go. The directory will be created if it does not exist. [required]
- --discard-unmapped
Exclude unmapped reads from cached BAM files. [default: not set]
GENERAL OPTIONS
- -t, --threads INT
Number of threads for mapping and sorting. [default:
1]
- -h, --help
Output a short usage message. [default: not set]
- --full-help
Output a full help message and display in 'man'. [default: not set]
- --full-help-roff
Output a full help message in raw ROFF format for conversion to other formats. [default: not set]
- -v, --verbose
Print extra debugging information. [default: not set]
- -q, --quiet
Unless there is an error, do not print log messages. [default: not set]
EXIT STATUS
- 0
Successful program execution.
- 1
Unsuccessful program execution.
- 101
The program panicked.