121. CleaveLand
A pipeline for using degradome data to find cleaved small RNA targets.
标签:MiRNA
122. VAAST
Variant Annotation, Analysis and Search Tool
标签:Structural variation
123. SNIP-Seq
Tool for discovering SNPs in population sequencing data
标签:SNP discovery
124. SolexaQA
User-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual...
标签:
125. Segemehl
Map short reads to known genome with tolerance for mismatches and indels using suffix arrays for high accuracy matching
标签:Genomics
126. ShoRAH
Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that expl...
标签:Metagenomics
127. CRISP
Identifies rare and common variants in pooled sequencing data
标签:SNP discovery
128. BSMAP
short reads mapping software for bisulfite sequencing
标签:DNA methylation
129. NPS
Identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.
标签:Epigenomics, ChIP-Seq
130. Myrna
Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets.
标签:RNA-Seq Quantitation, RNA-Seq Alignment
131. Solas
Given gene annotation the major questions addressed by the package are: prediction of alternative exons in a single condition / cell sample, prediction of differential alternative exons between two conditions / cell samples, quantification of alternative splice forms in a single conditi...
标签:RNA-Seq Quantitation,Alternative Splicing
132. SOCS
SOLiD reference based, un-gapped alignment with bisulfite capability
标签:RNA-Seq Alignment, DNA methylation, SNP discovery
133. MUMmerGPU
MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by HTS.
标签:Genomics, Transcriptomics
134. SeqAn
C++ template library with many sequence analysis algorithms and datastructures.
标签:Sequence analysis, Genomics,Phylogenetics
135. HawkEye
An interactive visual analytics tool for genome assemblies.
标签:
136. BayesPeak
A Bayesian hidden Markov model to detect enriched locations in ChIP-seq data.
标签:ChIP-Seq
137. PatMaN
Patman searches for short patterns in large DNA databases, allowing for approximate matches. It is optimized for searching for many small pattern at the same time, for example microarray probes.
标签:
138. BS Seeker
Mapping tool for bisulfite treated reads
标签:Epigenomics
139. CNVer
CNVer is a method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. CNVer combines this information within a unified computational framework cal...
标签:Structural variation, Copy number estimation
140. YASS
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).
标签: