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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (172 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (628 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (789 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 (842 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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NanoSim: nanopore sequence read simulator based on statistical characterization.
By Jit 2536 days agowww.bcgsc.ca - NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides...Biological file format tutorial
By Jit 2537 days agobioinformatics.uconn.edu - This section explains some of the commonly used file formats in bioinformatics. The information provided here is basic and designed to help users to distinguish the difference between different formats. Please refer user manual or other information...SVfinder: Tool for detecting genomic rearrangement form DNA-seq data
By Robert M Willioms 2540 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 2541 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 2542 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 2542 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 2543 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 2544 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 2544 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 2545 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...
