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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (203 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 (873 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Magic-BLAST
By Shruti Paniwala 1744 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
By Jit 1746 days agogithub.com - ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. ProteoClade helps you analyze two...Phytozome v12.1: plant science community hub for accessing palnts genomic data
By Surabhi Chaudhary 1747 days agophytozome.jgi.doe.gov - Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as...JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 1747 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. https://github.com/tanghaibao/jcvi More at https://github.com/tanghaibao/jcvi/wikiApollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
By BioStar 1748 days agogithub.com - Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described by Firtina et al. (preliminary version...GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns
By Neel 1749 days agogdblab.com - GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction. GSP4PDB is part of the services provided by the Bioinformatic Group of the University of...Sequence Tube Maps: displays multiple genomic sequences in the form of a tube map
By Jit 1754 days agogithub.com - A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg. (https://github.com/vgteam/vg) Link to working demo:...SvABA: Structural variation and indel detection by local assembly
By Jit 1754 days agogithub.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....GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 1757 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...U-Plot: Genome U-Plot sample implementation
By Rahul Nayak 1761 days agogithub.com - The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.
