BWA REST

BWA on XSEDE

BWA is the Burroughs-Wheeler Alignment tool for DNA sequencing.

The interface currently runs indexing, then BWA mem.

bwa -p index -a is ref_genome.fasta
&& bwa mem -M -t 16 -p ref_genome.fasta query1.fq.gz > aln.sam

Let us know if you need other options.

tool=BWA_XSEDE

Input files:
dbin_ = Infile Database sequences (FASTA format)
queryin­_ = InFile Query File 1 query1.fq.gz
queryinpair_ = InFile Query File 2 (paired reads) query2.fq.gz

Parameters:
tool=BWA_XSEDE
runtime_ - Float - Maximum Hours to Run (default 0.25)
SAM_NAME_ = String - Output File Name (default=aln.sam)
Pvalue_ = Switch - Submitting a single interleaved fastq? (default=0)
indexalg_ = Excl - Indexing algorithm (default=is or bwtsw)
colorspace_ = Switch - Build color-space index (default=0))
Pvalue2_ = Switch - Submitting a single interleaved fastq? (default=0))