http://last.cbrc.jp/ - LAST can:
Handle big sequence data, e.g:
Compare two vertebrate genomes
Align billions of DNA reads to a genome
Indicate the reliability of each aligned column.
Use sequence quality data properly.
Compare DNA...
Our research group is primarily focused on the analysis of whole genome sequence data to identify genetic variation (primarily structural variation) and examine their potential functional impact in disease phenotypes. We are particularly interested...
Raphael Lab research is focused on Bioinformatics and Computational Biology.
Current research interests include next-generation DNA sequencing, structural variation, genome rearrangements in cancer and evolution, and network analysis of somatic...
www.bioconductor.org - Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of...
github.com - pyScaf orders contigs from genome assemblies utilising several types of information:
paired-end (PE) and/or mate-pair libraries (NGS-based mode)
long reads (NGS-based mode)
synteny to the genome of some related species (reference-based...
www.mgc.ac.cn - GenomeComp is a tool for summarizing, parsing and visualizing the genome wide sequence comparison results derived from voluminous BLAST textual output, so as to locate the rearrangements, insertions or deletions of genome segments between species or...
http://docs.bpipe.org/ - Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.
January 20th, 2016 - New! Bpipe 0.9.9 released!
Download latest, all
Documentation
Mailing List (Google...
github.com - methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent...
github.com - In a nutshell
Anvi’o is an analysis and visualization platform for ‘omics data.
Please find the methods paper here: https://peerj.com/articles/1319/
Anvi’o would not have been possible without the help of many people who...
github.com - Reads simulator
Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing...