BOL

http://meme-suite.org/ - Motif based sequence analysis suits  The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. The MEME Suite...

We are two groups of scientists doing frontier research in quantitative biology and biomedicine. The Bienko group is interested in exploring the fundamental design principles controlling how DNA is packed in the eukaryotic nucleus and its relation...

github.com - v0.0 by Glenn Hickey (hickey@soe.ucsc.edu) Progressive Cactus is a whole-genome alignment package. Requirements git gcc 4.2 or newer python 2.7 wget 64bit processor and build environment 150GB+ of memory on at least one machine when...

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with...

bedtools.readthedocs.io - Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For...

code.google.com - splitbam splits a BAM by chromosomes. Using the reference sequence dictionary (*.dict), it also creates some empty BAM files if no sam record was found for a chromosome. A pair of 'mock' SAM-Records can also be added to those empty BAMs to...

downloads.jbei.org - MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users can understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic...

github.com - GroopM is a metagenomic binning toolset. It leverages spatio-temoraldynamics (differential coverage) to accurately (and almost automatically)extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use:...

http://json.org/ - JSON (JavaScript Object Notation) is a lightweight data-interchange format. It is easy for humans to read and write. It is easy for machines to parse and generate. It is based on a subset of the JavaScript Programming...

journals.plos.org - To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads,...