Neel
Bioinformatics Beginner
Latest comments
- Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (166 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/
- LEGE on Coronavirus Resources ! (1161 days ago): The US government SARS-CoV-2 Interagency Group (SIG) developed a...
- LEGE on Coronavirus Resources ! (1161 days ago): Illumina toolkit for...
- Surabhi Chaudhary on Coronavirus Resources ! (1243 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
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Neel 1086 days agogithub.com - MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw...VolcaNoseR - Exploring volcano plots
By Neel 1148 days agohuygens.science.uva.nl - Plot volcano plots online .... VolcaNoseR - Exploring volcano plotsWAAFLE: a Workflow to Annotate Assemblies and Find LGT Events.
By Neel 1155 days agohuttenhower.sph.harvard.edu - Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial communities, including the human microbiome. While methods exist to identify LGTs from sequenced isolate genomes, identifying LGTs from community...biostarhandbook
By Neel 1182 days agowww.biostarhandbook.com - Nice book collection for bioinformatician ... highly recommended.Applying MinHash to cluster RNAseq samples
By Neel 1183 days agoivory.idyll.org - A kmer blog worth spending time onk-mers tutorial - classification and taxonomy
By Neel 1183 days agoivory.idyll.org - DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lot of time thinking about how to store k-mer graphs efficiently, discard redundant data, and count them efficiently. More recently, we've...QuasR: Quantification and annotation of short reads in R
By Neel 1196 days agowww.bioconductor.org - The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and...Calling variants in non-diploid systems
By Neel 1244 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 1244 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 1246 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...
