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http://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...

www.rstudio.com - Devtools makes package development a breeze: it works with R’s existing conventions for code structure, adding efficient tools to support the cycle of package development. With devtools, developing a package becomes so easy that it will be...

wiki.fysik.dtu.dk - SLURM workload manager software, a free open-source workload manager designed specifically to satisfy the demanding needs of high performance computing. This page is a HOWTO guide for setting up a SLURM installation, currently focused on a CentOS 7...

satsuma.sourceforge.net - Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes,...

bitbucket.org - RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It...

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...

4dgenome.research.chop.edu - Records in 4DGenome are compiled through comprehensive literature curation of experimentally-derived and computationally-predicted interactions. The current release contains 4,433,071 experimentally-derived and 3,605,176 computationally-predicted...

broadinstitute.github.io - Decoding SAM flags This utility makes it easy to identify what are the properties of a read based on its SAM flag value, or conversely, to find what the SAM Flag value would be for a given combination of properties. To decode a given SAM flag...

http://kaiju.binf.ku.dk/ - Kaiju is a program for the taxonomic classification of metagenomic high-throughput sequencing reads. Each read is directly assigned to a taxon within the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein...