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FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1457 days agogithub.com - FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by...cutadapt
By Radha Agarkar 3145 days agocutadapt.readthedocs.io - Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cleaning your data in this way is often required: Reads from small-RNA sequencing contain the...Grinder / Biogrinder - A versatile omics shotgun and amplicon sequencing read simulator
By Jit 2769 days agosourceforge.net - Grinder is a versatile program to create random shotgun and amplicon sequence libraries based on DNA, RNA or proteic reference sequences provided in a FASTA file. Grinder can produce genomic, metagenomic, transcriptomic, metatranscriptomic,...coursera genome assembly tutorial
By Jit 2584 days agogithub.com - Solutions to Coursera Genome Sequencing (Bioinformatics II)Genobuntu: A software package containing more than 70 software and packages oriented towards NGS...
By BioStar 2203 days agosourceforge.net - Genobuntu is a software package containing more than 70 software and packages oriented towards NGS. In its current version, Genobuntu supports pre assembly tools, genome assemblers as well as post assembly tools. Commonly used biological...Genome assembly forensics: finding the elusive mis-assembly
By Jit 2157 days agoamos.sourceforge.net - We present the first collection of tools aimed at automated genome assembly validation. This work formalizes several mechanisms for detecting mis-assemblies, and describes their implementation in our automated validation pipeline,...StringTie Transcript assembly and quantification for RNA-Seq
By Jit 1657 days agoccb.jhu.edu - StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length...BlobToolKit: A toolkit for genome assembly QC
By Jit 1767 days agoblobtoolkit.genomehubs.org - Filtering raw genomic datasets is essential to avoid chimeric assemblies and to increase the validity of sequence-based biological inference. BlobToolKit extends the BlobTools1/Blobology2 approach to simplify interactive and reproducible...Supernova: generates phased, whole-genome de novo assemblies from a Chromium-prepared library.
By Jit 1667 days agosupport.10xgenomics.com - Supernova generates phased, whole-genome de novo assemblies from a Chromium-prepared library. Please see Achieving Success with De Novo Assembly and System Requirements before creating your Chromium libraries for...Genome assembly training tutorial at Galaxy !
By Jit 1456 days ago Comments (1)training.galaxyproject.org - In this tutorial we assemble and annotate the genome of E. coli strain C-1. This strain is routinely used in experimental evolution studies involving bacteriophages. For instance, now classic works by Holly Wichman and Jim Bull (Bull 1997, Bull...
