This python program wraps Uproc and HMMER3 allowing for the fast identification of NGS reads that belong to HMMER PHMMs. It was designed to be used with the protein domains of the Plasomdium falciparum VAR gene family but could be used for other domain models. By leverageing the speed of Uproc and the sensitivity of HMMER we are able to quickly annotate longer reads to smaller domain profiles.
Options:
-h, --help show this help message and exit
-r READ1, --read1=READ1
the first fastq file
-R READ2, --read2=READ2
the second fastq file
-E EVALUE, --evalue=EVALUE
the E value to be fed to HMMER
-o OUTDIR, --outdir=OUTDIR
the output directory for files