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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (202 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (659 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (820 days ago): Sequencing coverage is defined as the average number of reads that covers...
- Neel on CheckM:Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes (872 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1523 days agogithub.com - Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary...G-NEST: The Gene NEighborhood Scoring Tool
By Neel 1554 days agogithub.com - The Gene NEighborhood Scoring Tool (G-NEST) combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all window sizes. Primary author of final code = William F. Martin....RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
By BioStar 1560 days agowww.rosettacommons.org - RosettaAntibodyDesign (RAbD) is a generalized framework for the design of antibodies, in which a user can easily tailor the run to their project needs. The algorithm is meant to sample the diverse sequence, structure, and binding space of...pggb: the pangenome graph builder
By biogeek 1566 days agogithub.com - This pangenome graph construction pipeline renders a collection of sequences into a pangenome graph (in the variation graph model). Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining...VICUNA: a software tool that enables consensus assembly of ultra-deep sequence derived from diverse...
By biogeek 1586 days agowww.broadinstitute.org - VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in...Clustergrammer is a web-based tool for visualizing high-dimensional data as an interactive and...
By BioStar 1587 days agogithub.com - Clustergrammer is a web-based tool for visualizing high-dimensional data (e.g. a matrix) as an interactive and shareable hierarchically clustered heatmap. Clustergrammer's front end (Clustergrammer-JS) is built using D3.js and its back-end...parallelLastz: Lastz with multi-threads support.
By BioStar 1589 days agogithub.com - Running Lastz (https://github.com/lastz/lastz) in parallel mode. This program is for single computer with multiple core processors. When the query file format is fasta, you can specify many threads to process it. It can reduce run time linearly,...chromatiblock: Scalable, whole-genome visualisation of structural changes in prokaryotes
By BioStar 1589 days agogithub.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...Sibelia: A comparative genomics tool
By BioStar 1589 days ago Comments (1)github.com - Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the...mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 1590 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...
