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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (636 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (1092 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (1253 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 (1305 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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UPGMA Worked Example
By Abhi 1605 days agowww.slimsuite.unsw.edu.au - The tabs below include a walkthrough of clustering 7 biological sequences (A-G) using the Unweighted Pair-Group Method with Arithmetic mean (UPGMA) method. Note that UPGMA is actually a generic method and thus the walkthrough could apply to any...Introduction to phylogenies in R
By Abhi 1605 days agowww.phytools.org - R phylogenetics is built on the contributed packages for phylogenetics in R, and there are many such packages. Let's begin today by installing a few critical packages, such as ape, phangorn, phytools, and geiger. To get the most recent CRAN version...RNA-seq workflow: gene-level exploratory analysis and differential expression
By Jit 1609 days agomaster.bioconductor.org - Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count...PaReBrick: PArallel REarrangements and BReaks identification toolkit
By Jit 1610 days agogithub.com - PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their...MMseqs2: ultra fast and sensitive sequence search and clustering suite
By Abhi 1612 days agogithub.com - MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin)...Code Golf
By Abhi 1612 days agohttps://code.golf/ - Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters. Since this is your first time here, I suggest starting with something simple like Fizz Buzz.OGDRAW - Draw Organelle Genome Maps
By Abhi 1613 days agochlorobox.mpimp-golm.mpg.de - OrganellarGenomeDRAW converts annotations in the GenBank or EMBL/ENA format into graphical maps. The input has to be a GenBank or EMBL/ENA flat file wherase the output can vary among several types of files....VolcaNoseR - Exploring volcano plots
By Neel 1618 days agohuygens.science.uva.nl - Plot volcano plots online .... VolcaNoseR - Exploring volcano plotsWAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1625 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...Getting Started with Nextflow
By LEGE 1630 days agocarpentries-incubator.github.io - Introduction to Bioinformatics workflows with Nextflow and nf-core Getting Started with Nextflow Objectives Understand What a workflow management system is. Understand the benefits of using a workflow management system. Explain the benefits of...
