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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 (629 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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Bioinformatics lectures !
By Jit 2555 days agorob-p.github.io - Computational Biology is a huge field of study, that touches upon many distinct algorithmic and biological areas of study. What we are able to cover in this course will depend, in part, on the pace at which we move, which I will attempt to...Computational Genomics: Applied Comparative Genomics
By Jit 2556 days agogithub.com - The primary goal of the course is for students to be grounded in theory and leave the course empowered to conduct independent genomic analyses. We will study the leading computational and quantitative approaches for comparing and analyzing...Oxford Nanopore Sequencing, Hybrid Error Correction, and de novo Assembly of a Eukaryotic Genome
By Jit 2556 days agoschatzlab.cshl.edu - Monitoring the progress of DNA molecules through a membrane pore has been postulated as a method for sequencing DNA for several decades. Recently, a nanopore-based sequencing instrument, the Oxford Nanopore MinION, has become available that we used...simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
By Jit 2556 days agowww.ebi.ac.uk - simNGS is software for simulating observations from Illumina sequencing machines using the statistical models behind the AYB base-calling software. By default, observations only incorporate noise due to sequencing and do not incorporate effects from...DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing
By Robert M Willioms 2557 days agocompcytogen.pensoft.net - "DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and idiogram drawing as well as number of useful functions facilitating the procedure...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 2557 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...Opera: An optimal genome scaffolding program
By Jit 2557 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
By Jit 2557 days agokiwi.cs.dal.ca - RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositional classifications from a Naive Bayes classifier, RITA is able to...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2557 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...coursera genome assembly tutorial
By Jit 2559 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)
