Circlator: automated circularization of genome assemblies using long sequencing reads
A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Ci...ng long sequencing reads", Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: 1...2234 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing r...ults (Martin et al., WhatsHap: fast and accurate read-based phasing)...l with Illumina, PacBio, Oxford Nanopore and other typ...l It is easy to use: Pass in a VCF and one...2221 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of...able for the web. Feature information and rendering options are supplie...mplete with labels, a title, legends, and footnotes...the CGView gallery. http://wishart.biology.ualberta.ca/cgview/gallery.ht...2198 days ago
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies
KAT is a suite of tools that analyse jellyfish hashes or sequen...K-mers found given a GC count and a K-mer count. comp: K-mer c...nce file. blob: Given, reads and an assembly, calculates both...ting tools to visualise K-mer and compare distributions. The fo...ief details of how to install and use KAT....2033 days ago
NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
NextSV, a meta SV caller and a computational pipeline to perform SV calling from low...sequencing data. NextSV integrates three aligners and three SV callers and generates two inte...easily perform downstream annotation using ANNOVAR and dis...2150 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide...on and copy number pipelines, and has support for tumor samples...o;PureCN: Copy number calling and SNV class....” Source Code for Biology and Medicine, 11, 13. do...2148 days ago
FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
FMLRC, or FM-index Long Read Corrector, is a tool for performin...read sequencing using the BWT and FM-index of short-read sequen...FMLRC will build an FM-index and use that as an implicit de Br...uency k-mers in the long read and replacing them with the closest matchin...w complexity regions that are computa...2146 days ago
NanoPack: visualizing and processing long-read sequencing data
The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License....together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Wi...tools. https://academic.oup.com/bioinfo...2146 days ago
Snakemake—a scalable bioinformatics workflow engine
Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow.2123 days ago
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