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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (167 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (623 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (784 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 (836 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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StringTie Transcript assembly and quantification for RNA-Seq
By Jit 1627 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...Merqury: reference-free quality and phasing assessment for genome assemblies
By Jit 1630 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...HNADOCK: a nucleic acid docking server for modeling RNA/DNA–RNA/DNA 3D complex structures
By Poonam Mahapatra 1632 days agohuanglab.phys.hust.edu.cn - The HNADOCK server is to predict the binding complex structure between two nucleic acid molecules through a hierarchical docking algorihtm of an FFT-based global search strategy and an intrinsic scoring function for nucleic acid interactions. Users...ShinyGO v0.61: Gene Ontology Enrichment Analysis + more
By Jit 1633 days agobioinformatics.sdstate.edu - 2/3/2020: Now published by Bioinformatics. 11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more. 5/20/2019: V.0.60, Annotation database updated to Ensembl 96. New bacterial and fungal...gggenes: a ggplot2 extension for drawing gene arrow maps.
By BioStar 1634 days agohttp://wilkox.org/gggenes - Install the stable version of gggenes from CRAN: install.packages("gggenes") If you want the development version, install it from GitHub: devtools::install_github("wilkox/gggenes") More at https://github.com/wilkox/gggenesSynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.
By Jit 1636 days agosynvisio.github.io - SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images. SynVisio requires two files to run: The simplified gff file that was used as an...Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 1636 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1639 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Mercator: Multiple Whole-Genome Orthology Map Construction
By Jit 1648 days agowww.biostat.wisc.edu - Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an...Genobuntu: Package for Next Generation Sequencing and Genome Assembly
By BioStar 1649 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools.Commonly used biological software and...
