Neel
Bioinformatics Beginner
Latest comments
- 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/
- LEGE on Coronavirus Resources ! (1631 days ago): The US government SARS-CoV-2 Interagency Group (SIG) developed a...
- LEGE on Coronavirus Resources ! (1631 days ago): Illumina toolkit for...
- Surabhi Chaudhary on Coronavirus Resources ! (1713 days ago): Some important resources here https://artic.network/ncov-2019
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Genome, Bioinformatics, NGS, Assembly, Tool, Reads, Sequence, data, Tutorial, Plot, Analysis, Software, Pipeline, package, Alignment, R, sequencing, Tools, Sequences, structural, docking, DNA, virus, find, Annotation, Comparative, Genomics, variant, BAM, Perl, nanopore, program, CoVID, fast, accurate, visualize, rna, PacBio, SNP, Learn, Visualization, user-friendly, Assemblies, Gene, files, FASTQ, genomic, Mapping, Stats, CISA
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Neel's bookmarks
Calling variants in non-diploid systems
By Neel 1714 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 1714 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 1716 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...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1717 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 1717 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...CoverM: Read coverage calculator for metagenomics
By Neel 1771 days agogithub.com - CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. CoverM calculates coverage of genomes/MAGs coverm genome (help) or individual...A simple tutorial for a complex ComplexHeatmap
By Neel 1799 days agogithub.com - ComplexHeatmap (Gu, Eils, and Schlesner (2016)) is an R Programming Language (R Core Team (2020)) package that is currently listed in the Bioconductor package repository. install and load required packages...FiNGS: Filters for Next Generation Sequencing
By Neel 1833 days agogithub.com - Key features Filters SNVs from any variant caller to remove false positives Calculates metrics based on BAM files and provides filtering not possible with other tools Fully user-configurable filtering (including which filters to use and their...flutter
By Neel 1862 days agohttps://flutter.dev/ - Flutter is Google’s UI toolkit for building beautiful, natively compiled applications for mobile, web, and desktop from a single codebase.maftools : Summarize, Analyze and Visualize MAF Files
By Neel 1899 days agowww.bioconductor.org - With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widely accepted and used to store somatic variants detected. The Cancer Genome Atlas Project has sequenced over 30 different cancers with sample size of...
