BioStar
Bioinformatician
Our Sponsors
Related items
Common steps for reads mapping !
By BioStar 1247 days agoMapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.TARDIS: Toolkit for automated and rapid discovery of structural variants
By Neel 3346 days agogithub.com - tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone...CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS...
By BioJoker 2676 days agowww.nature.com - Validated a widely accessible approach that can be used to establish functional causality for noncoding sequence variants identified by GWASs. https://www.nature.com/articles/nm.3975MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer...
By Rahul Nayak 1563 days agogithub.com - MUM&Co is able to detect:Deletions, insertions, tandem duplications and tandem contractions (>=50bp & <=150kb)Inversions (>=1kb) and translocations (>=10kb)Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 3031 days agogithub.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...MSAProbs - Parallel and accurate multiple sequence alignment
By Neel 2585 days agomsaprobs.sourceforge.net - MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior...CLARK: Fast, accurate and versatile sequence classification system
By Jit 2365 days agoclark.cs.ucr.edu - CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to...dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 340 days agogithub.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...RapClust: Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence...
By Rahul Nayak 2863 days agogithub.com - RapClust is a tool for clustering contigs from de novo transcriptome assemblies. RapClust is designed to be run downstream of the Sailfish or Salmon tools for rapid transcript-level quantification. Specifically,...
