BOL

www.grnpedia.org - TRRUST contains 8,444 and 6,552 TF-target regulatory relationships of 800 human TFs and 828 mouse TFs, respectively. They have been derived from 11,237 pubmed articles, which describe small-scale experimental studies of transcriptional regulations....

www.broadinstitute.org - DISCOVAR is a new variant caller and DISCOVAR de novo a new genome assembler, both designed for state-of-the-art data. Their inputs are chosen to optimize quality while keeping costs low. Currently it takes as input Illumina reads of length 250 or...

www.nature.com - The human genome is arguably the most complete mammalian reference assembly yet more than 160 euchromatic gaps remain and aspects of its structural variation remain poorly understood ten years after its completion. The results in this paper...

genome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vt

github.com - A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics Authors: Qiyun Zhu (qiyunzhu@gmail.com), Katharina Dittmar...

novelseq.sourceforge.net - The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

pubmed.ncbi.nlm.nih.gov - This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering...

github.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...

github.com - Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector...

github.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...