NAME
coverm make - Generate BAM files through mapping (version: 0.7.0)
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), strobealign index (with--strobealign-use-index), or BWA index stem (with-p bwa-mem/bwa-mem2). [required]
MAPPING ALGORITHM OPTIONS
-p, --mapper NAME
| name | description |
|---|---|
minimap2-sr |
minimap2 with '-x sr' option |
bwa-mem |
bwa mem using default parameters |
bwa-mem2 |
bwa-mem2 using default parameters |
minimap2-ont |
minimap2 with '-x map-ont' option |
minimap2-pb |
minimap2 with '-x map-pb' option |
minimap2-hifi |
minimap2 with '-x map-hifi' 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 or BWA-MEM2. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]
- --strobealign-params PARAMS
Extra parameters to provide to strobealign. Note that usage of this parameter has security implications if untrusted input is specified. [default: none]
- --strobealign-use-index
Use a pregenerated index (one that has been created with 'strobealign --create-index'). The --reference option should be specified as the original FASTA file i.e. 'ref.fna' not 'ref.fna.r100.sti' [default: not set]
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]
FREQUENTLY ASKED QUESTIONS (FAQ)
Can the temporary directory used be changed? CoverM makes use of the system temporary directory (often /tmp) to store intermediate files. This can cause problems if the amount of storage available there is small or used by many programs. To fix, set the TMPDIR environment variable e.g. to set it to use the current directory: TMPDIR=. coverm genome <etc>
For thresholding arguments e.g. \-\-dereplication\-ani and \-\-min\-read\-percent\-identity, should a percentage (e.g 97%) or fraction (e.g. 0.97) be specified? Either is fine, CoverM determines which is being used by virtue of being less than or greater than 1.
EXIT STATUS
- 0
Successful program execution.
- 1
Unsuccessful program execution.
- 101
The program panicked.
EXAMPLES
- Map pair of read files to the combined_genomes.fna reference, storing sorted BAM files in output_dir/
$ coverm make -r combined_genomes.fna -1 read1.fq -2 read2.fq -o output_dir