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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (816 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1273 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1434 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 (1486 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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BRaVa Browser
By Jitendra Narayan 11 days agonikbaya.github.io - BRaVa Browser is an interactive web tool for exploring rare genetic variant associations. It allows users to search and visualize rare variant association results across genes and traits, making it easier to investigate potential relationships...Genomic Basis of Evolutionary Innovations (GEvol)
By BioStar 271 days agog-evol.uni-muenster.de - The Priority Programme (SPP 2349) funded by German Science Foundation (DFG) started 2022: „Genomic Basis of Evolutionary Innovations (GEvol)“ GEvol is unique as it will use, for the first time, a large taxonomic group to focus on one...WinPCA
By LEGE 345 days agogithub.com - A package for windowed principal component analysis. WinPCA performs principal component analyses (PCA) in sliding windows along chromosomes. Both hard-called genotypes (input: VCF or TSV) or genotype likelihoods (input: VCF, TSV or BEAGLE)...Termal: a fast and interactive terminal-based viewer for multiple sequence alignments
By LEGE 345 days agogithub.com - termal, a fast, interactive, terminal-based viewer for multiple sequence alignments (MSAs), designed for use on remote systems such as high-performance computing (HPC)...HiTE: a fast and accurate dynamic boundary adjustment approach for full-length Transposable...
By LEGE 348 days agogithub.com - HiTE is a Python software that uses a dynamic boundary adjustment approach to detect and annotate full-length Transposable Elements in Genome Assemblies. In comparison to other tools, HiTE demonstrates superior performance in detecting a...PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis
By LEGE 367 days agogithub.com - This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a...geNomad: Identification of mobile genetic elements
By LEGE 368 days agoportal.nersc.gov - geNomad is a tool that identifies virus and plasmid genomes from nucleotide sequences. It provides state-of-the-art classification performance and can be used to quickly find mobile genetic elements from genomes, metagenomes, or metatranscriptomes.Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences
By LEGE 368 days agogithub.com - Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.dna2bit: an ultra-fast and accurate genomic distance estimation software
By LEGE 368 days agogithub.com - dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation. It has been thoroughly tested using the g++ and clang compilers on both Linux and...GrAnnoT
By LEGE 368 days agoforge.ird.fr - GrAnnoT is an annotation transfer tool for pangenome graphs. It can transfer linear genome annotations to a pangenome graph containing the genome, and also transfer the pangenome graph's annotations on the genomes it contains. It also outputs...
