“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from R...h only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all2175 days ago
LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)
...probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's g...2196 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
...mosome-scale de novo genome assemblies without the need for laborious in vivo cloning steps. Further information about fragScaff, including source code, is available at:https://sour...2196 days ago
2195 days ago
bpRNA: large-scale automated annotation and analysis of RNA secondary structure
...nce, and flanking base pairs of each such structural feature. The bpRNA code is written in perl and requir...module. Several additional scripts for analysis are included. The source code is available at http://github...2187 days ago
WhatsHap: fast and accurate read-based phasing
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for lon...2182 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements s...t version, first run the following commands: cd SALSA make To run the code, you will need Python 2.7, BO...2164 days ago
JBrowse: Embeddable genome browser built completely with JavaScript and HTML5
...demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting da...2150 days ago
PureCN: copy number calling and SNV classification using targeted short read sequencing
...C, Chiang D, Morrissey M (2016). “PureCN: Copy number calling and SNV classification using targeted short read sequencing.” Source Code for Biology and Medicine,&nbs...2109 days ago
mmgenome: Tools for extracting individual genomes from metagneomes
The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the...2108 days ago