BOL

In this protocol, we address and describe the de novo assembly method for small to medium-sized genomes.

You will have some previous experience with genome bioinformatics or other large scale scientific data analysis, or a newly qualified graduate student with data science skills interested in DNA sequence data. While desirable, previous experience...

Assembly and Genome record pages now redirect to new NCBI Datasets pages.

pbil.univ-lyon1.fr - DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from...

Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following...

github.com - ReMILO, a reference assisted misassembly detection algorithm that uses both short reads and PacBio SMRT long reads. ReMILO aligns the initial short reads to both the contigs and reference genome, and then constructs a novel data structure called...

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 - VCF2PopTree is a client-side software written in Javascript and it runs purely within the user’s computer/browser.  VCF2PopTree is compatible with all population browsers including Chrome, Opera, Edge and Firefox and works equally...

static.ciscall.org - cisMuton is a caller that detects SNVs/indels by comparing target (foreground) and control (background) samples. cisMuton calls mutations from target capture regions, which are defined by the overlapping regions...

bix.ucsd.edu - BLASR (Basic Local Alignment with Successive Refinement) for mapping Single Molecule Sequencing (SMS) reads that are thousands to tens of thousands of bases long with divergence between the read and genome dominated by insertion and deletion...