usage: sixgill_build [-h] [--minlength MINLENGTH]

[--minqualscore MINQUALSCORE] [--metagenefile METAGENEFILE] [--minmetagenescore MINMETAGENESCORE] [--minorflength MINORFLENGTH] [--minlongesttryppeplen MINLONGESTTRYPPEPLEN] [--maxreads MAXREADS] [--minreadcount MINREADCOUNT] --out OUT [--outfasta OUTFASTA] [--debug] fastqfiles [fastqfiles ...]

Read in one or more fastq files. For each read, do a 6-frame translation and add all metapeptides that pass the specified filtering criteria. If --metagenefile is specified, start with the output of MetaGene Annotator instead of raw reads.

positional arguments:

fastqfiles input fastq file(s), bgzipped

optional arguments:

-h, --help	show this help message and exit
--minlength MINLENGTH
	min AA length of a metapeptide
--minqualscore MINQUALSCORE
	min base-call phred score across any NT in a metapeptide
--metagenefile METAGENEFILE
	input MetaGene Annotator output file. Records must be in same linear order as reads in fastqfiles
--minmetagenescore MINMETAGENESCORE
	minimum MetaGene score
--minorflength MINORFLENGTH
	min length of ORF-portion
--minlongesttryppeplen MINLONGESTTRYPPEPLEN
	minimum length of the longest tryptic peptide
--maxreads MAXREADS
	stop early if we hit this many reads
--minreadcount MINREADCOUNT
	minimum read count
--out OUT	Output metapeptide database file
--outfasta OUTFASTA
	Output metapeptide fasta database file
--debug	Enable debug logging