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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (639 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1096 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1257 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 (1309 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
By Robert M Willioms 3007 days agogithub.com - SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.TeachEnG: Teaching Engine for Genomics
By Jit 3008 days agoteacheng.illinois.edu - TeachEnG (pronounced “teaching”), a Teaching Engine for Genomics, provides educational games to help students and researchers understand key bioinformatics concepts. The current version includes interactive modules for sequence alignment...Mash: fast genome and metagenome distance estimation using MinHash
By Jit 3009 days agogithub.com - Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems or for development. Mash requires c++11 to build, which is...MashMap: a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to...
By Jit 3009 days ago Comments (1)github.com - MashMap is a fast and approximate software for mapping long reads (PacBio/ONT) or assembly to reference genome(s). It maps a query sequence against a reference region if and only if its estimated alignment identity is above a specified threshold. It...BBTools User Guide
By Neel 3011 days agojgi.doe.gov - The guides describe the function, syntax, and typical use-cases of the tools; for a complete list of parameters, run the tool’s shellscript or open it with a text editor. Most tools do not currently have a guide, but each has shellscripts with...Synima: Synteny Imaging tool
By Jit 3011 days agogithub.com - Synteny Imaging tool (Synima) written in Perl, which uses the graphical features of R. Synima takes orthologues computed from reciprocal best BLAST hits or OrthoMCL, and DAGchainer, and outputs an overview of genome-wide synteny in PDF. Each of...R googleVis examples
By Rahul Nayak 3012 days agocran.r-project.org - It may take a little while to load all charts. Please be patient. All charts require an Internet connection. These examples are taken from the googleVis demo. You can execute the demo via library(googleVis) demo(googleVis) For more details...MOSS: A System for Detecting Software Similarity
By Jit 3013 days agotheory.stanford.edu - Moss (for a Measure Of Software Similarity) is an automatic system for determining the similarity of programs. To date, the main application of Moss has been in detecting plagiarism in programming classes. Since its development in 1994, Moss has...Mugsy: multiple whole genome alignment tool
By Jit 3013 days ago Comments (1)mugsy.sourceforge.net - Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee....kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference...
By Jit 3013 days agosourceforge.net - Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages...
