DeepSeq Data Analysis Tools
| NGS Data Analysis |
|
| Site Name |
Description |
Clicks |
| FASTX Tool Kit |
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. |
144 |
| 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 realigner”. |
136 |
| 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". |
133 |
| 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". |
175 |
| 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". |
125 |
|
| 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. |
151 |
| 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. |
124 |
| Genome2Seq |
"Genome2Seq is used to rapidly retrieve a fasta file of sequences based on genome co-ordinates generated from RNA-Seq data". |
124 |
| 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". |
114 |
| 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". |
121 |
| 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. |
126 |
| Gene Ontology Tools |
"Gene
Ontology (GO), the de facto standard in gene functionality description,
is used widely in functional annotation and enrichment analysis". |
153 |
| 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. |
115 |
| 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". |
154 |
| 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. |
180 |
|
| 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". |
578 |
| 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
databases”. It can be used “to create a small laboratory database of
genome annotations, or a large web-accessible community database”. |
118 |
| 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". |
117 |
|
Metagenomics
| Metagenomics |
|
| Site Name |
Description |
Clicks |
| MEGAN4-MEtaGenome ANalyzer |
It is a "stand-alone analysis tool for metagenomic of short-read data". |
144 |
| 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. |
131 |
| 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 samples”. |
152 |
| 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". |
129 |
| 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". |
146 |
| Terragenome |
Its an international soil metagenome sequencing consortium. |
135 |
|
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