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.
Accurately discover viral integration events and fusion transcripts by the use of soft-clipping information, read-pair analysis, and targeted de novo assembly
"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. "
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
kisSnp compares two sets of NGS raw reads, detecting Single Nucleotide Polymorphism occurring between the two sets. The two sets typically come from the sequencing of two individuals from the same species or from closely related species.
标签：Comparative genomics,Comparative transcriptomics,Gene annotation retrieval, SNP discovery, InDel discovery
ngs_backbone is a bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. It is capable of cleaning reads, do de novo assembly or mapping against a reference and annotate SNPs, SSRs, ORFs, GO terms and sequence descr...
"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...
Samscope is a lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data as intuitive as Google Maps. Samscope uses multiple layers to simultaneously (or sequentially) view SAM/BAM related features like coverage or allele frequency, or ChIP-SEQ feature...
Circos is tool for visualizing data in a circular format. It was developed for genomic data but can work for many other kinds of data as well.
Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for explor...
discoSnps : qualitative de-novo SNP caller. Extremely low memory and time efficient. No reference genome needed. Call both homozygous and heterozygous SNPs.
标签：Population Genomics,Comparative genomics,Barcoding, DNA-Seq, De novo assembly, Genotyping, High-throughput sequencing
Processes raw sequence data from Sanger or 454 sequencing into a hybrid de-novo assembly, annotates it and produces GMOD compatible output, including a SeqFeature database suitable for GBrowse.
Genome Trax™ enables you to identify human genome variations of functional significance by mapping your NGS data to known elements such as disease mutations and regulatory sites.