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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (637 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1093 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1254 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 (1306 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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JCVI:Python utility libraries on genome assembly, annotation and comparative genomics
By Jit 2181 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 2182 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 2183 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 2187 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 2188 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 2191 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 2195 days agogithub.com - The Genome U-Plot is a JavaScript tool to visualize Chromosomal abnormalities in the Human Genome using a U-shape layout.DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution
By Rahul Nayak 2195 days agosysomics.com - DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. Ab initio training could be performed according to our published...shinyChromosome:a GUI for the interactive creation of non-circular whole genome diagrams
By Jit 2198 days agoyimingyu.shinyapps.io - shinyChromosome is a graphical user interface for interactive creation of non-circular whole genome diagrams developed using the R Shiny package. To create single-genome plot by aligning genome data along all chromosomes of a single genome, go to...RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS...
By Surabhi Chaudhary 2198 days agogithub.com - RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows. Single-SNP GWAS with RGWAS.normal function SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests...
