Using arachne

usage
arachne command options... inputs...

Use --help or -h or call arachne without arguments to call up the docstring.

Arachne comes with three commands, generally intended to be used in this order:

convert FASTQ files to Standard format (requires samtools to be available on your PATH)

arachne preprocess [-t] PREFIX r1.fq r2.fq

index the reference FASTA to be used for alignment (bwa index wrapper)

arachne index ref.fa

align FASTQ files to reference FASTA

arachne align [options] ref.fa r1.fq r2.fq

[Under construction]