RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes....1714 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existi...ution time of short sequence alignment, a crucial step in analyzing sequenced genomes....1706 days ago
simuG: a general-purpose genome simulator
Simulated genomes with pre-defined and random genomic variants can be very useful for benchmarking genomic and bioinformatics analyses. Here we introduce simuG, a l...1682 days ago
HaploTypo: a variant-calling pipeline for phased genomes
...increasing number of phased (i.e. with resolved haplotypes) reference genomes are available. However, most...loTypo, a pipeline tailored to resolve haplotypes in genetic variation analyses. HaploTypo infers the haploty...1661 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gain...f gene order along chromosomes, for large data sets including dozens of whole genomes...1645 days ago
De novo Genome Assembly for Illumina Data
Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introducti...discuss and outline the process of de novo assembly for small to medium sized genomes....1629 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standar...gap filling tools PBJelly and GMcloser. gapFinisher can fill gaps in draft genomes...1625 days ago
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Genome in a Bottle (GIAB) Consortium
The Genome in a Bottle (GIAB) Consortium is a public-private-academic consortium hosted by NIST to develop the tech...//www.nist.gov/news-events/news/2016/09/nist-releases-new-family-standardized-genomes1623 days ago
Kevler: Reference-free variant discovery in large eukaryotic genomes
Welcome to kevlar, software for predicting de novo genetic variants without mapping reads to a reference genome! kevlar's k-mer abundance based metho...1621 days ago