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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (635 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1092 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1253 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 (1305 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Genomic Basis of Evolutionary Innovations (GEvol)
By BioStar 90 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 164 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 164 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 166 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 186 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 187 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 187 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 187 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 187 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...GFAffix : Identifies walk-preserving shared affixes in variation graphs and collapses them into a...
By BioStar 190 days agogithub.com - GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
