• 资源导航
41. Scripture
Tool for assembling transcriptome from paired-end Illumina RNA-Seq data
标签：RNA-Seq Alignment
42. 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
43. SHRiMP
Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. Works with data in letterspace (Roche, Illumina), colourspace (AB) and Helicos space. SHRiMP2 ...
标签：
44. GMAP
GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences.
标签：
45. ANNOVAR
ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data
标签：Genomics, Genetics
46. SOAPsnp
SOAPsnp is an accurate consensus sequence builder based on soap1 and SOAPaligner/soap2's alignment output. It calculates a quality score for each consensus base, which can be used for any latter process to call SNPs.
标签：SNP discovery
47. EDENA
An assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Previous version now edena2
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48. Shore
Analysis suite for short read data.
标签：Structural variation, SNP discovery
49. SSA
SSA (Signal Search Analysis) is a software package for the analysis of nucleic acid sequence motifs that are postionally correlated with a functional site (e.g a transcription or translation initiation site).
标签：Motif analysis
50. RMAP
Assembles 20 - 64 bp Solexa reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.
标签：DNA methylation
51. SeqTrim
A pipeline for preprocessing sequences.
标签：
52. VarScan
VarScan, an open source tool for variant detection that is compatible with several short read align-ers.
标签：SNP discovery
53. ERGO Genome Analysis and Discovery System
ERGO provides a systems-biology informatics toolkit centered on comparative genomics to capture, query and visualize sequenced genomes. Building upon the most comprehensive genomic database available anywhere integrated with the largest collection of microbial metabolic and non-metaboli...
标签：Metabolic reconstruction,Phylogenetics, Comparative genomics, SNP Annotation, SNP discovery, Alignment, Exome analysis, Metagenomics,Pathway analysis, Comparative transcriptomics, Functional Genomics, Gene Expression Analysis, Genome Wide Association Stud
54. Biopython
Biopython provides a tool kit for writing bioinformatics and computational molecular biology software in Python.
标签：Sequence analysis,Phylogenetics, Population genetics, Protein structures
55. SeqSeg
An algorithm to identify chromosomal breakpoints using massively parallel sequence data
标签：Copy number estimation
56. BreakDancer
BreakDancer is an application for detecting structural rearrangements and indels in short read sequencing data BreakDancer, released under GPLv3, is a Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. It include...
标签：Genomics, Structural variation, InDel discovery
57. BFAST
Blat-like Fast Accurate Search Tool.
标签：Whole Genome Resequencing
58. VariationHunter
Detection of structural rearrangements
标签：Structural variation
59. SSAKE
The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to help leverage the in...
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60. Trinity
Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. RNA-Seq De novo Assembly
标签：De novo transcriptome assembly
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