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Alignment-free sequence comparison tools available for next-generation sequencing data analysis
Last updated 3041 days ago by Abhimanyu Singh Comments (1)kallisto Transcript abundance quantification from RNA-seq data (uses pseudoalignment for rapid determination of read compatibility with targets) Software (C++) https://pachterlab.github.io/kallisto/ Sailfish Estimation of isoform abundances...SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
By BioStar 2027 days agogithub.com - SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large...INC-Seq: accurate single molecule reads using nanopore sequencing
By Jit 3021 days agogithub.com - INC-Seq reads enabled accurate species-level classification, identification of species at 0.1 % abundance and robust quantification of relative abundances, providing a cheap and effective approach for pathogen detection and microbiome profiling...HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
By Rahul Nayak 2859 days agogithub.com - HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for...Circlator: automated circularization of genome assemblies using long sequencing reads
By Poonam Mahapatra 2852 days agosanger-pathogens.github.io - A tool to circularize genome assemblies. The algorithm and benchmarks are described in the Genome Biology manuscript. Citation: "Circlator: automated circularization of genome assemblies using long sequencing reads", Hunt et al, Genome Biology...Flye: Fast and accurate de novo assembler for single molecule sequencing reads
By Rahul Nayak 2435 days agogithub.com - Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The...FastProNGS: fast preprocessing of next-generation sequencing reads
By Rahul Nayak 1896 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...CovCal: Coverage / Read Count Calculator
By Jit 3550 days ago Comments (1)apps.bioconnector.virginia.edu - Coverage / Read Count Calculator Calculate how much sequencing you need to hit a target depth of coverage (or vice versa). Instructions: set the read length/configuration and genome size, then select what you want to calculate. Written by Stephen...AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing
By BioStar 2996 days agosourceforge.net - AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to...MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
By Rahul Nayak 2856 days agogithub.com - MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correction algorithms that are much more efficient than the state of art of aligners and...
