MPscan (multi-pattern scan) is a program for mapping short reads (<30bp) exactly on a set of reference sequences (eg, a genome) without indexing the reference. MPscan performs only exact mapping (no substitution, nor indels), is fast (optimal complexity), and easy to use.
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...
Array Studio is a complete analysis and visualization package for NextGen sequencing data, as well as other -OMIC data types. Array Server is a backend enterprise server for storage and analysis of -OMIC and NextGen sequencing data.
The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each ...
"BioRuby comes with a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, for the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many wide...
The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
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...
Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Cortex allows de novo assembly of variants without having to do a consensus assembly first. Also allows comparison of genomes without using consensus, and alignment of sequence data to ...
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.
FastQ Screen provides a simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.
The Vancouver Short Read Analysis Package (VSRAP) contains the FindPeaks application for Chip-Seq and RNA-Seq analysis, as well as utilities for SNP finding, working with aligned sequence files and a nascent database for storing SNPs across multiple libraries.