1. Phred
2. Blat
Fast, accurate spliced alignment of DNA sequences Blast-like Alignment Tool to perform rapid mRNA/DNA and cross-species protein alaignments. BLAT (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California S...
3. Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner. Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. The new version has programs with a 2 in the name eg bowtie2 Bowtie, an...
标签:Sequence database search
4. SAMtools
Various utilities for processing alignments in the SAM format, including variant calling and alignment viewing. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. ...
标签:SNP discovery
5. BWA
Fast, accurate, memory-efficient aligner for short and long sequencing reads Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. BWA is a software package for mapping lo...
标签:Mapping, Read alignment
ERANGE is a Python package for doing RNA-seq and ChIP-seq.
标签:RNA-Seq Alignment, RNA-Seq Quantitation, ChIP-Seq,Allele-specific transcription
Includes GAP4, GAP5, SPIN, TREV, and numerous smaller tools. Used mainly for sequencing projects but also has other functions. Initialize with the command staden_new for the current X-Windows version inclduing gap5. staden sets up the previous version.
8. velvet
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD Sequence assembler for very short reads: commands velveth and velvetg Velvet is a de novo genomic assembler specially designed for short read sequencing te...
标签:De-novo assembly
9. MUMmer
MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing differen...
10. Maq
Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Maq stands for Mapping and Assembly with Quality. It builds assembly by mapping short reads to reference ...
标签:Genomics, SNP discovery
11. SOAP
SOAP (Short Oligonucleotide Alignment Program) is a program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. SOAP2 is an updated program based on Burrows-Wheeler Transform. has been in evolution from a single alignment tool to a tool pac...
标签:SNP discovery
12. CHiPSeq
From Science Johnson, 2007
13. Mauve
Mauve Genome Alignment software, for comparing two or more draft or finished genomes
标签:Genomics, Transcriptomics
14. TopHat
TopHat is a fast splice junction mapper for RNA-Seq reads. A fast splice junction mapper for RNA-seq reads that uses bowtie (see above) s a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read al...
标签:RNA-Seq Alignment
15. macs
Model-based Analysis of ChIP-Seq data. Model-based Analysis of ChIP-Seq (MACS): for identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of bindi...
16. EdgeR
edgeR is an R/Bioconductor software package for statistical analysis of replicated count data. Methods are designed for assessing differential expression in comparative RNA-Seq experiments, but are generally applicable to count data from other genome-scale platforms (ChIP-Seq, MeDIP-Seq...
标签:RNA-Seq, RNA-Seq Quantitation,ChIP-Seq, Gene Expression Analysis, DNA methylation
17. CuffLinks
Cufflinks assembles transcripts and estimates their abundances in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support ...
标签:RNA-Seq Alignment, RNA-Seq Quantitation, Alternative Splicing, Transcriptome, RNA-Seq
18. Abyss
ABySS is a de novo sequence assembler designed for short reads and large genomes. A de novo short read assembler for small or large genomes ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for asse...
标签:De-novo assembly
Metagenome Analysis Software - MEGAN (“MEtaGenome ANalyzer”) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another compar...
20. GATK
The Genome Analysis Toolkit (GATK) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers. The GATK solves the data management challenge by separating data access patterns from analysis algorit...
标签:SNP discovery