ngs_SPAdes

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.