Neel
Bioinformatics Beginner
Latest comments
- Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (178 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/
- LEGE on Coronavirus Resources ! (1173 days ago): The US government SARS-CoV-2 Interagency Group (SIG) developed a...
- LEGE on Coronavirus Resources ! (1173 days ago): Illumina toolkit for...
- Surabhi Chaudhary on Coronavirus Resources ! (1255 days ago): Some important resources here https://artic.network/ncov-2019
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Genome, Bioinformatics, NGS, Assembly, Tool, Reads, Sequence, Tutorial, Plot, Analysis, data, Pipeline, package, Software, Alignment, R, sequencing, Tools, structural, docking, DNA, virus, find, Annotation, Comparative, Genomics, Sequences, variant, BAM, Perl, nanopore, program, CoVID, fast, accurate, visualize, rna, PacBio, SNP, Learn, Visualization, user-friendly, Assemblies, Gene, files, FASTQ, Mapping, Stats, CISA, rapid
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Neel's bookmarks
LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1259 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 1259 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 1314 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 1341 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 1375 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 1404 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 1441 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...SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
By Neel 1444 days agogithub.com - The first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. SneakySnake greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short...Liftoff: An accurate GFF3/GTF lift over pipeline
By Neel 1444 days agogithub.com - Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...COVID Moonshot: An international effort to DISCOVER A COVID ANTIVIRAL
By Neel 1444 days agocovid.postera.ai - The COVID Moonshot is an ambitious crowdsourced initiative to accelerate the development of a COVID antiviral. We work in the open with no intellectual property constraints. This way, any scientist can view submitted drug designs and experimental...
