BOL

gitlab.com - CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It...

github.com - This is a tool for detecting structural variations using soft-clipping information From SAM files. https://github.com/shinout/clipcrop

github.com - To create a fresh environment for chromatiblock to run in do: conda create --name chromatiblock conda activate chromatiblock conda install chromatiblock --channel conda-forge --channel bioconda Then in future to run chromatiblock you can...

github.com - Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT). It is designed for matching tumor/normal analysis, supports multiple tumor samples, and produces accurate and complete somatic and germline calls. Severus...

github.com - Structural variant comparison tool for VCFs Given benchmark and comparsion sets of SVs, calculate the recall, precision, and f-measure. Spiral Genetics Motivation

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...

github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...

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...

sourceforge.net - Cerulean extends contigs assembled using short read datasets like Illumina paired-end reads using long reads like PacBio RS long reads. Cerulean v0.1 has been implemented with bacterial genomes in mind. The method is fully described in...