资源导航

1. MIRA: MIRA 3 - Whole Genome Shotgun and EST Sequence Assembler Whole Genome Shotgun and EST sequence assembler; 标签：De-novo assembly, SNP discovery, RNA-Seq Alignment
2. SeqMan NGen: Sequence assembly software using traditional, next-gen, and third-gen techonologies. Subsequent analysis of the assembly, including SNP discovery, coverage evaluation and consensus annotation is provided through full integration with Lasergene.; 标签：Genomics, De-novo assembly, De novo transcriptome assembly,Whole Genome Resequencing, SNP discovery, InDel discovery,ChIP-Seq, RNA-Seq Alignment
3. USeq: Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations; 标签：ChIP-Seq, RNA-Seq Alignment
4. 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
5. Novocraft: Novoalign is a program for mapping short reads from the Illumina/SOLiD sequencing platform(s) to a reference genome. Package for aligning short reads to reference genomes; 标签：Genomics, Whole Genome Resequencing, RNA-Seq Alignment, ChIP-Seq, MiRNA
6. MapNext: 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 ...; 标签：SNP discovery, RNA-Seq Alignment
7. OLego: OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapp...; 标签：Genomics, RNA-Seq, RNA-Seq Alignment
8. BBMap: 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
9. Subjunc: The Subread read aligner and Subjunc junction detector employ a novel read mapping paradigm called "seed-and-vote" to achieve a fast mapping speed and a high mapping accuracy. The seed-and-vote paradigm is particularly powerful in detecting indels. Subjunc can be used to discover exon-e...; 标签：Alternative Splicing, Next-generation sequencing, RNA-Seq Alignment

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