BOL

www.ici.upmc.fr - ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network and it can be used in combination with GOlorize. The identifiers can be uploaded from a text file or...

github.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...

lbbe.univ-lyon1.fr - SEX-DETector is a probabilistic method that relies on RNAseq data from a cross (parents and progeny of each sex) to infer autosomal and sex-linked genes (genes located on the non recombining part of sex chromosomes). How does SEX-DETector...

github.com - ShadowCaster implements an evolutionary model to calculate Bayesian likelihoods for each ‘alien genes’ with an unusual sequence composition according to the host genome background to detect HGT events in...

omega.omicsbio.org - Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph...

github.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...

www.ncbi.nlm.nih.gov - RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can...

hibberdlab.com - Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This...

github.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....

www.darwintreeoflife.org - The specimens were collected by the Oxford Wytham Woods and Edinburgh Lohse lab teams. DNA extraction and sequencing was carried out by the Sanger Institute Scientific Operations teams. Assemblies were carried out by the Tree of Life team (Shane...