BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically esti...
标签：SNP discovery, Genotyping, DNA methylation, Bisulfite Sequencing
MapNext provides four mainly analysis: (i) unspliced alignment and clustering of reads, (ii) spliced alignment of transcriptomic reads, (iii) SNP detection and calculation of SNP frequency from population sequences, and (iv) storage of result data into database to make it available for ...
BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels.
标签：Resequencing, Alignment,Quality Control, RNA-Seq Alignment, Alternative Splicing, Whole Genome Resequencing, SNP discovery,Phylogenetics, Metagenomics,Read Binning
CoNAn-SNV is a probabilistic framework for the discovery of single nucleotide variants in WGSS data. This software explicitly integrates information about copy number state of different genomic segments into the inference of single nucleotide variants.
kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.
标签：Comparative genomics,Comparative transcriptomics,Gene annotation retrieval, SNP discovery, InDel discovery
The Genomatix Mining Station (GMS) offers mapping of NGS reads onto genomes, transcriptomes and splice-junction libraries. It is a client-server based solution and can be controlled through an intuitive GUI or via command-line. It covers different tasks such as, as genomic positioning, ...
ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descr...