Metaxa uses Hidden Markov Models to identify, extract and classify small-subunit (SSU) rRNA sequences (12S/16S/18S) of bacterial, archaeal, eukaryotic, chloroplast and mitochondrial origin in metagenomes and other large sequence sets
标签：Metagenomics, Phylogenetics,Sequence analysis, Community analysis
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
User-friendly, web-based analytical pipeline for comparative metagenomic studies. Input can be derived from either 16S rRNA data or NextGen shotgun sequencing.
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
The Ribosomal Database Project's Pyrosequencing Pipeline aims to simplify the processing of large 16s rRNA sequence libraries obtained through pyrosequencing. This site processes and converts the data to formats suitable for common ecological and statistical packages such as SPADE, Esti...
"FHiTINGS is designed for use in rapidly identifying, classifying, and parsing internal transcribed spacer (ITS) DNA sequences after a BLASTn search. This software is useful for fungal ecology studies using next generation sequencing (NGS)."
Genometa is a Java based local bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been cons...
Search, organize and analyze genomic and protein information of any size via desktop program that provides publication ready images to enhance the impact of your research.
标签：Phylogenetics, Sequence analysis, De-novo assembly,Genomics, Population genetics,Metagenomics, Structural variation, RNA-Seq,Epigenomics
Mapsembler is a targeted assembly software. It takes as input a set of NGS raw reads and a set of input sequences (starters). It first determines if each starter is read-coherent, e.g. whether reads confirm the presence of each starter in the original sequence. Then for each read-cohere...
de novo and reference assembly of Roche/454, Illumina and SOLiD data. Uses a novel Condensation Assembly Tool approach where reads are joined via "anchors" into mini-contigs before assembly which reduces sequencing errors. Requires Win or MacOS.
标签：De novo sequencing,Metagenomics, SNP discovery,InDel discovery, Targeted resequencing
Comprehensive analysis pipelines powered with unique mapping speed and sensitivity deliver deep genomic analysis in variant detection and metagenomic applications with Illumina, Ion Torrent, Complete Genomics and Roche 454 data sets.
标签：Exome and whole genome variant detection, Metagenomics, SNP discovery, InDel discovery