riboPicker is a publicly available tool that is able to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. riboPicker is available as both standalone and web-based versions.
Megraft is a software tool to graft ribosomal small subunit (16S/18S) fragments from metagenomes onto full-length SSU sequences, enabling accurate diversity estimates from fragmentary and non-overlapping sequence data.
标签：Metagenomics, Phylogenetics,Sequence analysis, Community analysis, Rarefaction
Tripal is a collection of open-source, freely-available Drupal modules that serves as a web interface for a GMOD Chado database. It is designed to allow anyone with genomic data to quickly create an online genomic database using community supported tools. Tripal is part of the open-sour...
The MethPipe software package is a computational pipeline for analyzing bisulfite sequencing data (BS-seq, WGBS and RRBS). MethPipe provides tools for mapping bisulfite sequencing read and estimating methylation levels at individual cytosine sites. Additionally, MethPipe includes tools ...
标签：Epigenomics, DNA methylation,Bisulfite Sequencing
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...
Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly
User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.
"BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. "
A free genome browser for exploring sequencing pile-up and coverage data with numerous annotation tracks hosted on the cloud.
标签：Sequence analysis, DNA-Seq,Alignment, De novo sequencing,Exome analysis, Exome and whole genome variant detection, Genetics, Whole Genome Resequencing, Next Generation Sequencing,Genomics
Copy number analysis for exome-sequencing / targeted-resequencing. Two methods of analysis available: Case vs Control, or Case vs Baseline. Function available for creating a baseline from multiple samples.
标签：Next Generation Sequencing,Cancer biology, Genomics, Copy number estimation
"BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to f...
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