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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (199 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (656 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (817 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 (869 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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bacLIFE: an automated genome mining tool for identification of lifestyle associated genes
By BioStar 285 days agogithub.com - bacLIFE is a streamlined computational workflow that annotates bacterial genomes and performs large-scale comparative genomics to predict bacterial lifestyles and to pinpoint candidate genes, denominated lifestyle-associated genes (LAGs), and...UniAligner: a parameter-free framework for fast sequence alignment
By Abhi 291 days agogithub.com - UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces a sequence-dependent alignment scoring that automatically changes for any pair of compared sequences. Classical alignment approaches,...doubletrouble: identify duplicated genes from whole-genome protein sequences and classify
By LEGE 295 days agobioconductor.org - doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal...OMArk: software for proteome (protein-coding gene repertoire) quality assessment
By LEGE 307 days agogithub.com - OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence...CLAW: Chloroplast Long-read Assembly Workflow
By LEGE 308 days agogithub.com - CLAW (Chloroplast Long-read Assembly Workflow) is an mostly-automated Snakemake-based workflow for the assembly of chloroplast genomes. CLAW uses chloroplast long-reads, which are baited out of larger read libraries (e.g., an Oxford Nanopore...pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
By LEGE 308 days agogithub.com - ausarg/pipesnake is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across...PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
By LEGE 308 days agogithub.com - What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs...Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
By LEGE 308 days agogithub.com - Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA files...PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked...
By LEGE 328 days agogithub.com - PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It...ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
By LEGE 377 days agoacademic.oup.com - ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing...
