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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (165 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (622 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (783 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 (835 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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Variant Calling Pipeline
By LEGE 33 days agogithub.com - The variantcalling.nf nextflow script will take any number of samples with paired-end reads in FASTQ format, map reads using Bowtie2, process BAM files, and finally call variants using BCFtools v1.21 and/or Freebayes v1.3.6. If part of the...SVbyEye: R Package to visualize alignments between two or multiple DNA sequences
By LEGE 65 days agogithub.com - R Package to visualize alignments between two or multiple DNA sequences includinga number of functionalities to facilitate processing of alignments in PAF format. SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence...LoVis4u: Locus Visualisation tool for comparative genomics
By LEGE 65 days agogithub.com - Description LoVis4u is a bioinformatics tool for Loci Visualisation. LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualisation of multiple genomic loci. LoVis4u generates vector images in...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 65 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic...
By LEGE 72 days agogithub.com - NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of...Modern Statistics with R
By LEGE 91 days agowww.modernstatisticswithr.com - This is the online version of the second edition of Modern Statistics with R. It is free to use, and always will be. Printed copies are available from CRC Press. Live online courses on statistics with R based on this book,...Dengue Lineages !
By LEGE 97 days agodengue-lineages.org - Our dengue virus lineage system splits up the current genotypes into major and minor lineages to provide additional spatiotemporal resolution and a common language to discuss important genomic diversity. A full description of the lineage system can...HELIANO: A fast and accurate tool for detection of Helitron-like elements
By LEGE 100 days agogithub.com - Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging...1000 Genomes Chile Project
By LEGE 105 days agohttps://1000genomas.cl/ - Welcome to Chile Sequence to Chile: A Genomic Exploration Project for the Future Genomics, the science that deciphers the complexity of DNA, immerses us in the world of life at its most basic level. On this journey into the depths of genetic...GenoFig: a user-friendly application for the visualization and comparison of genomic regions
By BioStar 107 days agoforgemia.inra.fr - Tool for graphical vizualisation of annotated genetic regions, and homologous regions comparison. It is an independent recoding of Easyfig 2 initially developped by at the S. Beatson Lab [https://mjsull.github.io/Easyfig/] Download the GenoFig...
