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Bowtie
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Aligns short read geared toward mammalian re-sequencing. Bowtie is based on a Burrows-Wheeler index based on the full-text minute-space (FM) index. It follows two steps: an initial, ungapped seed-finding stage that derives advantage from the speed and memory efficiency of the full-text minute index and a gapped extension stage that employs dynamic programming and benefits from the efficiency of single-instruction multiple-data (SIMD) parallel processing available on modern processors.
GNUMAP / Genomic Next-generation Universal MAPper
Offers a platform dedicated to map next generation sequencing (NGS) data. GNUMAP combines a Needleman–Wunsch method, statistical mapping algorithms and a full-text index in minute space (FM-index). The application leverages additional information to enhance exploitable data. It is able to determine spike regions in the reference genome as well as to manage repetitive regions. The results can be exported towards the UCSC Genome Browser or Affymetrix’s Integrated Genome Browser for further visualization.
SCRAM / Small Complementary RNA Mapper
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Consists of an integrated alignment and visualization suite. SCRAM uses algorithms for exact matching of reads to reference sequences. This tool performs two classes of alignment: (1) a “compare’ alignment”, where the aggregate aligned read count and standard error for each individual miRNA or longer reference sequence is generated for two treatments or genotypes; and (2) a “profile’ alignment”, where position-by-position alignment data for each individual reference sequence is generated for a single treatment or genotype.
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