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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (169 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (625 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (786 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 (839 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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svelter
By Jitendra Prajapati 3191 days agogithub.com - This software is designed to identify both simple and complex rearrangements from paired-end sequencing data. Users could ran it easily by just alling SVelter.py with proper parameters. It's also possible to ran it on multiple cores by...Ensembl comparative genomics resources
By Jitendra Narayan 3192 days agowww.ncbi.nlm.nih.gov - The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny,...Stacks
By Jitendra Narayan 3196 days agocatchenlab.life.illinois.edu - Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps...Genome Browser : GBrowse
By Jit 3201 days agoelp.ucdavis.edu - Generic Genome Browser Version 2: A Tutorial for Administrators This is an extensive tutorial to take you through the main features and gotchas of configuring GBrowse as a server. This tutorial assumes that you have successfully set up Perl, GD,...BioToolbox
By Jit 3201 days agocpansearch.perl.org - This is a collection of libraries and high-quality end-user scripts for bioinformatic analysis, including working with gene annotation, collecting data scores from a variety of modern file formats, and conversion between file formats. The...Advanced Bash-Scripting Guide
By Jit 3202 days agotldp.org - This tutorial assumes no previous knowledge of scripting or programming, yet progresses rapidly toward an intermediate/advanced level of instruction . . . all the while sneaking in little nuggets of UNIX® wisdom and lore. It serves as a...UCSC Genome Browser and Blat software !
By Jit 3202 days agohgdownload.cse.ucsc.edu - This directory contains Genome Browser and Blat application binaries built for standalone command-line use on various supported Linux and UNIX platforms. To determine which set of binaries to download, type "uname -a" on the command line to display...HiCdat
By Jit 3208 days agogithub.com - HiCdat: a fast and easy-to-use Hi-C data analysis tool HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes,...Centurion
By Jit 3208 days agocbio.ensmp.fr - Although centromeres are essential for life and are the subject of extensive research, centromere locations in yeast genomes are difficult to infer, and in most species they are still unknown. Recently, the chromatin conformation assay Hi-C has been...NCBI Remap
By Jit 3209 days agowww.ncbi.nlm.nih.gov - NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use...
