Bwa single end reads
It is made for resequencing projects, namely in a diagnostic setting. GMAP: longer reads, with multiple indels and splices (see entry above under Genomics analysis); GSNAP: shorter reads, with one indel or up to two splices per read.Useful for digital gene expression, SNP and indel genotyping. Used by the National Center for Genome Resources (NCGR) in Alpheus.Many standalone biological applications (mapper, split mapper, mappability, and other) provided.Fast, accurate overlap assembler with the ability to handle any combination of sequencing technology, read length, any pairing orientations, with any spacer size for the pairing, with or without a reference genome.
Computes Smith-Waterman gapped alignments and mapping qualities on one or more GPUs. Processes 100,000 to 500,000 reads per second (varies with data, hardware, and configured sensitivity).Quantify and manage large quantities of short-read sequence data.CASHX pipeline contains a set of tools that can be used together, or separately as modules.This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment.See structural alignment software for structural alignment of proteins.