Penn SCAP-T Pipeline: Documentation
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Module: SPAdes
Runs SPAdes using the trimmed files from sampleID/trim.
Usage:
ngs.sh SPAdes [-i inputDir] -p numProc -m maxRAM -k kmers [-se] sampleID
Input:
sampleID/inputDir/unaligned_1.fq
sampleID/inputDir/unaligned_2.fq (paired-end reads)
Output:
sampleID/SPAdes/SampleID.fasta
Requires:
SPAdes ( http://bioinf.spbau.ru/spades )
Options:
-i inputDir - location of source files (default: trim).
-p numProc - number of cpu to use.
-k kmers (default: 33,49,83) --> SPAdes
-m maximum RAM (default: 250)
-se - single-end reads (default: paired-end)
Runs SPAdes using the trimmed files from sampleID/trim. Output is stored in sampleID/SPAdes.