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21. SOAPdenovo
SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds.
標(biāo)簽：De-novo assembly
22. SSAHA
SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences.
標(biāo)簽：
23. MG-RAST
MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison
標(biāo)簽：Metagenomics,?Phylogenetics,Metabolic reconstruction
24. DESeq
DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The latest version is DESeq2 (released April 2013).
標(biāo)簽：RNA-Seq Quantitation,?ChIP-Seq
25. PyroNoise
Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis.
標(biāo)簽：Phylogenetics,?Metagenomics
26. seqmonk
A tool to visualise and analyse high throughput mapped sequence data SeqMonk is a program to enable the visualisation and analysis of mapped sequence data
標(biāo)簽：Genomics,?Epigenomics
27. CisGenome
An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
標(biāo)簽：ChIP-Seq,?ChIP-on-chip,?Motif analysis,?Gene annotation retrieval
28. BWA-SW
Fast, accurate, memory-efficient aligner for long sequencing reads
標(biāo)簽：Mapping,?Read alignment
29. ALLPATHS
De novo assembly of whole-genome shotgun microreads.
標(biāo)簽：De-novo assembly
30. Standalone hamming
Example software for decoding error-correcting barcodes
標(biāo)簽：
31. QuEST
QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
標(biāo)簽：ChIP-Seq
32. exonerate
Various forms of alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX. A generic tool for pairwise sequence comparison A generic tool for pairwise sequence comparison
標(biāo)簽：
33. BEDTools
BEDTools is an extensive suite of utilities for comparing genomic features in BED format. A powerful toolset for genome arithmetic.
標(biāo)簽：Genomics
34. IGV
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types and format, including short-read alignments in the SAM/BAM format. Data can be viewed from local files or ov...
標(biāo)簽：Genomics
35. MiRDeep
Discovering known and novel miRNAs from deep sequencing data
標(biāo)簽：MiRNA
36. Sissrs
Produce a list of peakmaxima from aligned positions.
標(biāo)簽：ChIP-Seq
37. Arachne
ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments.
標(biāo)簽：
38. Batman
Bayesian tool for methylation analysis (Batman) ??for analyzing methylated DNA immunoprecipitation (MeDIP) profiles
標(biāo)簽：DNA methylation
39. MrFAST
mrFAST is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.
標(biāo)簽：Genomics
40. BiQ Analyzer
BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data. With more than 2,000 downloads so far, BiQ Analyzer has become a standard tool for processing DNA methylation data from bisulfite sequencing.
標(biāo)簽：Epigenomics,?DNA methylation