cmuts align¶

Purpose¶

Aligning raw sequencing data against the reference library.

Requires¶

One or more FASTQ files containing the sequenced reads
The FASTA library

As well as both minimap2 and samtools on the path, and fastp for paired-end input.

Usage¶

One invocation handles one sample. Pass a single FASTQ file for single-end reads,

cmuts align -f references.fasta -o treated.bam -x map-ont treated.fastq

or two for paired-end reads.

cmuts align -f references.fasta -o treated.bam -x sr treated_R1.fastq.gz treated_R2.fastq.gz

Merging¶

Paired-end input is merged with fastp before alignment. A pair whose mates do not overlap cannot be merged and is discarded. fastp reports how many pairs it merged on standard error.

Presets¶

-x is required, and names the platform the reads came from, which is passed on to minimap2 for alignment purposes. The following lists common choices; consult the minimap2 documentation for all choices.

Preset	Platform
`sr`	Illumina, MGI, Complete Genomics
`map-ont`	Oxford Nanopore
`map-hifi`	PacBio HiFi
`map-pb`	PacBio CLR

Paired-end inputs are refused unless the preset is sr.

Options¶

Arguments¶

Argument	Description
`READS`	reads to align
`MATE`	the second file of a pair, merged with the first

Input and output¶

Option	Description
`-f, --fasta FASTA`	reference sequences, or a minimap2 index (required)
`-o, --output BAM`	write sorted alignments to this file (required)
`--overwrite`	replace the output file if it already exists

Alignment¶

Option	Description
`-x, --preset PRESET`	how minimap2 aligns (sr\|map-ont\|map-hifi\|map-pb) (required)

Performance¶

Option	Description
`-t, --threads N`	threads for merging, alignment and sorting (default 1)

Information¶

Option	Description
`-h, --help`	show this help and exit
`-V, --version`	show the version and exit