Latest comments
Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (201 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/- BioStar on Perl Module Installation (657 days ago): To install BioPerl on a macOS system, you can follow these steps: Open the...
- Abhi on CovCal: Coverage / Read Count Calculator (818 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 (871 days ago): MOre at https://bitbucket.org/berkeleylab/checkv/src/master/
Tag cloud
Bioinformatics, Genome, NGS, assembly, Analysis, tool, reads, Sequencing, Data, alignment, Sequence, Visualization, R, Pipeline, Computational Biology, Genomics, genomes, Annotation, Long, Tools, Tutorial, Software, Fast, Gene, DNA, Plot, sequences, Genomic, Assemblies, PacBio, Package, Assembler, de novo, Synteny, Learn, read, Chromosome, accurate, Interactive, Perl, nanopore, genes, Program, Web, Scaffolding, Database, Server, Python, Mapping, Comparative
Our Sponsors
All site bookmarks
Interactive Bioinformatics Resources !
By Jit 1233 days agohttp://sandbox.bio - Learn how to use bioinformatics tools right from your browser.Everything runs in a sandbox, so you can experiment all you want. More at sandbox.bioVentoy: an open source tool to create bootable USB drive
By LEGE 1276 days agogithub.com - Ventoy is an open source tool to create bootable USB drive for ISO/WIM/IMG/VHD(x)/EFI files. With ventoy, you don't need to format the disk over and over, you just need to copy the image files to the USB drive and boot it. You can copy many image...Calling variants in non-diploid systems
By Neel 1279 days ago Comments (1)training.galaxyproject.org - The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low frequency variants. Some of the early attempts to do this well have been...QuasiModo - Quasispecies Metric Determination on Omics
By Neel 1279 days agogithub.com - This repository contains the scripts and pipeline that reproduces the results of the HCMV benchmarking study. In this study we evaluated genome assemblers and variant callers on 10 in vitro generated, mixed strain HCMV sequence samples, each...Luigi: a Python package that helps you build complex pipelines of batch jobs.
By Neel 1281 days agogithub.com - Luigi is a Python (3.6, 3.7, 3.8, 3.9 tested) package that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization, handling failures, command line integration, and much more. Run pip...Pandoc: a universal document converter
By Surabhi Chaudhary 1282 days agohttps://pandoc.org/ - If you need to convert files from one markup format into another, pandoc is your swiss-army knife. Pandoc can convert almost all formats https://pandoc.org/index.htmlLoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1282 days ago Comments (1)academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...IVA: accurate de novo assembly of RNA virus genomes
By Neel 1282 days agogithub.com - IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected...JCVI utility libraries
By Jit 1328 days agogithub.com - Collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.Simons Genome Diversity Project
By Jit 1328 days agowww.simonsfoundation.org - Complete genome sequences from more than one hundred diverse human populations All genomes in the dataset were sequenced to at least 30x coverage using Illumina technology. The sequencing reads were mapped and genotyped using a customized procedure...
