DeepSeq Data Analysis Tools
| NGS Data Analysis |
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| Site Name |
Description |
Clicks |
| FASTX Tool Kit |
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
4660 |
| The Genome Analysis Toolkit (GATK) |
“The GATK is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it’s a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realignerâ€. |
3285 |
| Genome-wide Complex Trait Analysis (GCTA) |
"GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits". |
2825 |
| Burrows Wheeler Algorithm Download |
"BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads". |
3709 |
| SAM Tools |
"SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format". |
3577 |
| BFAST |
BFAST stands for "Blat-like Fast Accurate Search Tool ". "BFAST facilitates the fast and accurate mapping of short reads to reference sequences ". |
2552 |
| BWA |
"BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algorithm is designed for Illumina sequence reads up to 100bp, while the rest two for longer sequences ranged from 70bp to 1Mbp " |
3182 |
| Bowtie |
"Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small" |
3133 |
| VariationHunter |
"VariationHunter-CommonLaw is a tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies" |
2514 |
| mrFAST |
It is Micro Read Fast Alignment Search Tool. This tool is "designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner" |
2567 |
| SOAP Aligner |
"It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer" |
2914 |
| SOAPdenovo |
"SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads" |
3522 |
| SOAPsnp |
"The program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference" |
2914 |
| Celera Assembler/CABOG |
This is "is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing" |
2696 |
| BreakDancer |
BreakDancer-0.0.1 is a Perl package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads". It specifies the mapping quality threshold for ambiguous reads. |
2414 |
| CNVnator |
"It is a tool for CNV discovery and genotyping from depth of read mapping". CNVnator 3.0 is the latest version avialable. |
2671 |
| PEMer |
"PEMer package contains the computational codes and documentations for the algorithm developed to construct and analyze structural variants (SV)" |
2516 |
| VarScan |
This commandline based tool is used for "variant detection in massively parallel sequencing data". |
3944 |
| Allpaths-LG |
"This blog provides the latest news concerning ALLPATHS-LG, the new short read genome assembler from the Computational Research and Development group at the Broad Institute" |
3469 |
| Velvet |
It is a "Sequence assembler for very short reads", maintained by EBI. "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI)" |
4147 |
| SSAHA2 |
Sequence Search and Alignment by Hashing Algorithm (SSAHA2) "is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences". "SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package" |
2539 |
| String Graph Assembler (SGA) |
"SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads" |
3408 |
| IMPUTE2 |
"IMPUTE version 2 is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009". "IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes." |
10927 |
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Top of Page
| SNP Detection and Genomics Work |
|
| Site Name |
Description |
Clicks |
| GenSel Software |
BIGS GenSel Login Page. GelSel is used primarily for statistical analyses associated with Genomic Selection. This software was developed by Dr. Dorian J. Garrick and Dr. Rohan Fernando at Iowa State University, USA. |
3596 |
| AgBase v. 2.00 |
"AgBase is a curated resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations". It provides several functional analysis tools, including, GOProfiler, Genome2Seq, GORetriver etc. |
2813 |
| Genome2Seq |
"Genome2Seq is used to rapidly retrieve a fasta file of sequences based on genome co-ordinates generated from RNA-Seq data". |
2715 |
| gnuplot version 4.6 |
"gnuplot is a command-driven interactive function plotting program. It can be used to plot functions and data points in both two- and three-dimensional plots in many different formats. It is designed primarily for the visual display of scientific data. gnuplot is copyrighted, but freely distributable". |
2564 |
| SNPlotz: a genome plot tool for SNP association studies |
"SNPlotz is a web tool for users to plot phenotypic effects data from GWAS analysis, along a genome. The plot tool is coupled with the GBrowse to bring up all related genome features (transcripts, genes, QTL, etc) for further data mining on any interesting SNP shown on the plot". |
2681 |
| Bioinformatics Services and Tools- CCMB, MI, USA |
Use this website to get guidelines on workflows of RNAseq, ChipSeq, Genome Assembly, Genome RNAseq and microarray analysis as well as list of several useful bioinformatics tools and resources. |
2970 |
| Gene Ontology Tools |
"Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis". |
2803 |
| MISO-The Sequence Ontology Browser |
Its the "home page of the Sequence Ontology Project (SO), a joint effort by genome annotation centres, and other groups using sequence annotation data, including: WormBase, FlyBase, the Mouse Genome Informatics group, and the Sanger Institute". Aims at developing an ontology suitable for describing biological. |
2620 |
| SNP Nexus |
An SNP annotation tool. "SNPnexus was designed to simplify and assist in the selection of functionally relevant Single Nucleotide Polymorphisms (SNP) for large-scale genotyping studies of multifactorial disorders". |
3390 |
| Helix System |
This system "evaluates new high performance architectures and introduces them into production work at NIH". Some of the function of this system are installing scientific application programs, evaluateing new high performance architectures, installing and supporting scientific application programs etc. |
3203 |
| Samtools |
"SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments". "SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format". |
2795 |
| Beagle v. 3.3.2 |
"BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples". BEAGLE can be used for "phasing genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. infer sporadic missing genotype data", to "impute ungenotyped markers that have been genotyped in a reference panel", to "perform single marker and haplotypic association analysis" and to "detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals" |
3947 |
| Sniper |
It is "a Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads" |
2504 |
| GATK |
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance" |
3185 |
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Top of Page
| NGS Forums |
|
| Site Name |
Description |
Clicks |
| SEQanswers: Discussion Forum |
A discussion forum "intended to be oriented toward life sciences and next generation sequencing". However, "any scientific topic related to genomics is open for discussion". |
26034 |
| Generic Model Organism Database |
The Generic Model Organism Database project is “a collection of open source software tools for creating and managing genome-scale biological databasesâ€. It can be used “to create a small laboratory database of genome annotations, or a large web-accessible community databaseâ€. |
2595 |
| Database management for SNP data (snpdb) |
"This project is used to facilitate the management and analysis of Single-Nucleotide Polymorphism (SNP) data from Genome-Wide Association Studies (GWAS) using a database system". |
2628 |
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Top of Page
| Transcriptome Analysis |
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| Site Name |
Description |
Clicks |
| Myrna |
"Myrna is a cloud computing tool for calculating differential gene expression in large RNA-seq datasets. Myrna uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible" |
2675 |
| Cufflinks |
"Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation 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 each one, taking into account biases in library preparation protocols" |
3737 |
| Rnnotator |
"Rnnotator" software: To address challenges related to comprehensive annotation and quantification of transcriptomes, Rnnotator was developed by a team at the JGI to provide an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome" |
2241 |
| Genomic Short-read Nucleotide Alignment Program (GSNAP) |
Used for aligning short reads of transcripts. It has added feature of enbling the user to check "for and eliminating indel/splice combinations at ends of alignments", "finding of microexons in short reads" |
2578 |
| TopHat |
"TopHat is 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 aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons" |
5418 |
| Trinity |
Trinity "represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads" |
2423 |
| ERANGE |
"E-RANGE is our Python package for doing RNA-seq and ChIP-seq (hence the "dual-use"), and is a descendant of the ChIPSeq mini peak finder ". "ERANGE is not compatible with bowtie 0.9.9.X" |
56526 |
| Trans-Abyss |
"Trans-ABySS is a software package that is designed to analyze ABySS-assembled whole-genome shotgun transcriptome data" |
2441 |
| Scripture |
"Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio." |
2318 |
| RUM |
"RUM is an RNA-Seq alignment pipeline" |
2429 |
| G-Mo.R-Se |
G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. The "candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models" |
2362 |
| MapSplice |
It is used for "accurate mapping of RNA-seq reads for splice junction discovery". |
2381 |
| SpliceMap |
"SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths" |
2396 |
| Oases |
It is used for "De novo transcriptome assembler for very short reads". "Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly" |
3292 |
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Top of Page
| Functional Annotation |
|
| Site Name |
Description |
Clicks |
| SIFT |
"SIFT predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related sequences, collected through PSI-BLAST. SIFT can be applied to naturally occurring nonsynonymous polymorphisms or laboratory-induced missense mutations." |
4322 |
| Polyphen-2 |
"PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations". |
3367 |
| snpEff v. 3.5 |
"Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes)". |
2859 |
| ANNOVAR |
"ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others)". |
3304 |
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Top of Page
| CRISPR Cas |
|
| Site Name |
Description |
Clicks |
| Crispr Benchling |
This site provides a fast CRISPR gRNA designing tool with respect to specified gene or genome coordinates. The result also provide annotation on the exon and CDS information. |
2314 |
| Cas-OFFinder |
This tool identifies the possible off-target sites of Cas9 RNA-guided endonucleases. |
2277 |
| CCTop |
It's an online tool for CRISPR/Cas9 target prediction. Please go through the paper at doi: 10.1371/journal.pone.0124633 for detail. |
1659 |
| Genome Engineering Software Tools |
This page of Omictools provide a range of tools related to Crisp Cas, viz. pgRNADesign, MAGESTIC, ProtospacerWB etc. |
1419 |
| CHOPCHOP v.2 |
"CHOPCHOP is a web tool for selecting target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN-directed mutagenesis". Please refer to doi:10.1093/nar/gkw398 |
1510 |
| CRISPOR |
This tool is used for designing, evaluating and cloning guide sequences for the CRISPR/Cas9 system. |
1701 |
| CRISPR LifePipe |
To "design both gRNA and donor template sequences required for genome editing". |
1386 |
| sgRNA Designer |
"This tool ranks and picks candidate sgRNA sequences for the targets provided, while attempting to maximize on-target activity and minimizing off-target activity" |
1888 |
| DESKGEN |
This fully user customezable biocomputational tool-set is provided by Desktop Genetics group. |
1327 |
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Metagenomics
Top of Page
| Metagenomics |
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| Site Name |
Description |
Clicks |
| MEGAN4-MEtaGenome ANalyzer |
It is a "stand-alone analysis tool for metagenomic of short-read data". |
2944 |
| MG-RAST |
"MG-RAST (the Metagenomics RAST) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data". Its works the best in Firefox browser. |
2998 |
| IMG/M |
“The Integrated Microbial Genomes (IMG) system serves as a community resource for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. The IMG data warehouse integrates genome and metagenome datasets provided by IMG users with a comprehensive set of publicly available isolate and single cell genomes, and a rich set of publicly available metagenome samplesâ€. |
2671 |
| CAMERA |
CAMERA (Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis) aims at serving the" needs of the microbial ecology research community, and other scientists using metagenomics data, by creating a rich, distinctive data repository and a bioinformatics tools resource that will address many of the unique challenges of metagenomic analysis". |
2591 |
| CARMA |
"CARMA is a software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system". |
2674 |
| Terragenome |
Its an international soil metagenome sequencing consortium. |
3174 |
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