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The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
MIRA - Sequence assembler and mapper for whole genome shotgun and EST / RNASeq sequencing data. Can use Sanger, 454, Illumina and IonTorrent data. PacBio: CCS and ecCLR data usable, CLR not yet. Please visit http://sourceforge.net/apps/mediawiki/mira-assembler/
This library implements a thread-safe skip list data structure - a kind of list with good insertion, deletion and searching performances. It uses Fred Fish's dbug library as internal tracing/debugging system. See the web site for more details.
This is a library implementing skip lists for the Go programming language (http://golang.org/).Skip lists are a data structure that can be used in place of balanced trees. Skip lists use probabilistic balancing rather than strictly enforced balancing and as a result the algorithms for insertion and deletion in skip lists are much simpler and significantly faster than equivalent algorithms for balanced trees.
Web-based user interface for MAQ (Mapping and Assembly with Qualities), an Illumina / Solexa Deep Sequencing Reads (fastq format) mapping software. MAQGene classifies each found mutation based on its canonically predicted effect on the coding sequence.
This java command line application aligns Next-Generation Sequencing (NGS) reads very sensitive to reference sequences, accounting for large deletion, and removes indels, causing frame shifts. In addition, only specific regions can be considered.