Neel
Bioinformatics Beginner
Latest comments
- Abhi on LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data (637 days ago): Detail paper here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111061/
- LEGE on Coronavirus Resources ! (1632 days ago): The US government SARS-CoV-2 Interagency Group (SIG) developed a...
- LEGE on Coronavirus Resources ! (1633 days ago): Illumina toolkit for...
- Surabhi Chaudhary on Coronavirus Resources ! (1715 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
GenomeThreader: Gene Prediction Software
By Neel 2712 days agogenomethreader.org - GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via...STELLAR: fast and exact local alignments
By Neel 2747 days agowww.seqan.de - STELLAR is very practical and fast on very long sequences which makes it a suitable new tool for finding local alignments between genomic sequences under the edit distance model. Binaries are freely available for Linux, Windows, and Mac OS X...CBS Comparative Microbial Genomics group - BioTools download page
By Neel 2754 days agowww.cbs.dtu.dk - he CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a...Snippy: Rapid haploid variant calling and core SNP phylogeny
By Neel 2765 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 2766 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 2794 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 2825 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 2921 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 3008 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 3026 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,...
