• 资源导航
21. SOAPdenovo
SOAPdenovo, a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds.
标签：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.
标签：
23. MG-RAST
MG-RAST is a fully-automated service for annotating metagenome samples providing analysis tools for comparison
标签：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).
标签：RNA-Seq Quantitation, ChIP-Seq
25. PyroNoise
Clustering of pyrosequencing (454) data with noise model (AmpliconNoise) and chimaera removal (Perseus) for sequence diversity analysis.
标签：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
标签：Genomics, Epigenomics
27. CisGenome
An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
标签：ChIP-Seq, ChIP-on-chip, Motif analysis, Gene annotation retrieval
28. BWA-SW
Fast, accurate, memory-efficient aligner for long sequencing reads
标签：Mapping, Read alignment
29. ALLPATHS
De novo assembly of whole-genome shotgun microreads.
标签：De-novo assembly
30. Standalone hamming
Example software for decoding error-correcting barcodes
标签：
31. QuEST
QuEST is a Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitations (ChIP-Seq or ChIPseq).
标签：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
标签：
33. BEDTools
BEDTools is an extensive suite of utilities for comparing genomic features in BED format. A powerful toolset for genome arithmetic.
标签：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...
标签：Genomics
35. MiRDeep
Discovering known and novel miRNAs from deep sequencing data
标签：MiRNA
36. Sissrs
Produce a list of peakmaxima from aligned positions.
标签：ChIP-Seq
37. Arachne
ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments.
标签：
38. Batman
Bayesian tool for methylation analysis (Batman) €”for analyzing methylated DNA immunoprecipitation (MeDIP) profiles
标签：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.
标签：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.
标签：Epigenomics, DNA methylation
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