BBTools genomic aligner and other tools for short sequences

 The BBTools are a collection of small programs to solve recurrent
 tasks for the creative handling of short biological RNA/DNA sequences.
 This suite may be best known for its mapper, which is also the name of
 the project on sourceforge, but several tools have been added over time.
 All tools are multi-threaded, implemented platform-independently in Java:
 .
 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.
 .
 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.