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Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (209 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (666 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (827 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 (879 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
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mosdepth: fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
By Jit 1878 days agogithub.com - mosdepth can output: per-base depth about 2x as fast samtools depth--about 25 minutes of CPU time for a 30X genome.mean per-window depth given a window size--as would be used for CNV calling.the mean per-region given a BED file of regions.a...Bioinformatics web development course
By Jit 1885 days agowww.cellbiol.com - This web development course, targeted at Biology and Bioinformatics students, aims at teaching from scratch all the skills needed to setup a fully working Linux web server and to develop and deploy web applications for Bioinformatics. No previous...Dash: a web application framework that provides pure Python abstraction around HTML, CSS, and...
By Jit 1887 days agodash.plot.ly - Dash is a web application framework that provides pure Python abstraction around HTML, CSS, and JavaScript. Dash Bio is a suite of bioinformatics components that make it simpler to analyze and visualize bioinformatics data and interact with them in...Shouji: a fast and efficient pre-alignment filter for sequence alignment
By Jit 1887 days agogithub.com - The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration...Gooey: Turn (almost) any Python command line program into a full GUI application with one line
By BioStar 1891 days agogithub.com - Turn (almost) any Python command line program into a full GUI application with one line The easiest way to install Gooey is via pip pip install Gooey Alternatively, you can install Gooey by cloning the project to your local directory git...Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 1891 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
By Jit 1896 days agogithub.com - Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into...ALF--a simulation framework for genome evolution.
By Jit 1900 days agohttp://alfsim.org/#index - Artificial Life Framework (ALF) simulates a root genome into a number of related genomes. Result files include the resulting gene sequences, true tree and true MSAs. A description of ALF can be found in the following article: Daniel A Dalquen,...CONTIGuator !
By BioStar 1919 days agosourceforge.net - CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).alluvial diagram
By Jit 1932 days agocran.r-project.org - Alluvial diagram is a variant of a Parallel Coordinates Plot (PCP) but for categorical variables. Variables are assigned to vertical axes that are parallel. Values are represented with blocks on each axis. Observations are represented...
