BOL

www.well.ox.ac.uk - Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. It's recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of...

www.cbcb.umd.edu - Metagenomics sequencing projects collect samples of DNA from uncharacterized environments that may contain hundreds or even thousands of species. One of the main challenges in analyzing a metagenome is phylogenetic classification of raw sequence...

www.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....

journals.plos.org - Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) reads at a low cost. Even with low (advertised 1%) error rate, 100 × coverage Illumina data on average has an error in some read...

Mapping reads to a reference genome is an essential step in many types of genomic analysis, such as variant calling and gene expression analysis.

Benchmarking a new metagenomic pipeline often begins with a fundamental challenge. Imagine a bioinformatician preparing to benchmark a new metagenomic pipeline. There is no shortage of real sequencing data, but one problem quickly appears: the exact...

nikbaya.github.io - BRaVa Browser is an interactive web tool for exploring rare genetic variant associations. It allows users to search and visualize rare variant association results across genes and traits, making it easier to investigate potential relationships...

github.com - Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles...

github.com - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation...

github.com - MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being...