short read aligner and other bioinformatic tools

 BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling
 arbitrarily large genomes with millions of scaffolds. Handles Illumina,
 PacBio, 454, and other reads; very high sensitivity and tolerant of
 errors and numerous large indels.
 .
 BBMap is multithreaded as well as the other tools bundled into this
 package for instance:
 .
 BBNorm: Kmer-based error-correction and normalization tool.
 .
 Dedupe: Simplifies assemblies by removing duplicate or contained
 subsequences that share a target percent identity.
 .
 Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam,
 interleaved/paired, and ASCII-33/64, at over 500 MB/s.
 .
 BBDuk: Filters, trims, or masks reads with kmer matches to an
 artifact/contaminant file.