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 ! (1162 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
Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2294 days agogithub.com - Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). It will use as many CPUs as you can give it on a single computer (tested to 64 cores). It is...FMLRC: a long-read error correction tool using the multi-string Burrows Wheeler Transform
By Neel 2295 days agogithub.com - FMLRC, or FM-index Long Read Corrector, is a tool for performing hybrid correction of long read sequencing using the BWT and FM-index of short-read sequencing data. Given a BWT of the short-read sequencing data, FMLRC will build an FM-index and use...transrate: Understanding your transcriptome assembly
By Neel 2323 days agohibberdlab.com - Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This...RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
By Neel 2354 days agogithub.com - RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate single-enzyme digestion, double-enzyme digestion and size selection process. It can also analyze multiple genomes...Reference-free prediction of rearrangement breakpoint reads
By Neel 2450 days agocode.google.com - lideSort-BPR ( b reak p oint r eads) is based on a fast algorithm for all-against-all comparisons of short reads and theoretical analyses of the number of neighboring reads. When applied to a dataset with a sequencing...BBTools User Guide
By Neel 2537 days agojgi.doe.gov - The guides describe the function, syntax, and typical use-cases of the tools; for a complete list of parameters, run the tool’s shellscript or open it with a text editor. Most tools do not currently have a guide, but each has shellscripts with...SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
By Neel 2555 days agohciweb.iwr.uni-heidelberg.de - This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit,...LIBSVM -- A Library for Support Vector Machines
By Neel 2668 days agowww.csie.ntu.edu.tw - LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. Since version 2.8, it...TARDIS: Toolkit for automated and rapid discovery of structural variants
By Neel 2722 days agogithub.com - tardis Toolkit for Automated and Rapid DIscovery of Structural variants Requirements zlib (http://www.zlib.net)mrfast (https://github.com/BilkentCompGen/mrfast)htslib (included as submodule; http://htslib.org/)Fetching tardis git clone...NovelSeq: Novel Sequence Insertion Detection
By Neel 2722 days agonovelseq.sourceforge.net - The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726
