Penn SCAP-T Pipeline: Documentation
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Module: BLASTDB
This module will generate a Blast database using the raw (untrimmed) reads. The sampleID will be used as the name for the Blast database.
Usage:
ngs.sh blastdb [-se] sampleID
Input:
sampleID/orig/unaligned_1.fq
sampleID/orig/unaligned_2.fq (paired-end reads)
Output:
sampleID/blastdb/*
Requires:
makeblastdb ( ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ )
Options:
-se - single-end reads (default: paired-end)
Generates blast database from reads.