REAPR: a universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual insp...Tags: Bioinformatics, Computational Biology, Assembly, Comparison, Accuracy, Evaluation
2947 days ago
Tags: Bioinformatics, NGS, Assembly, Quality, FastQC, Tutorial
2939 days ago
Tags: Bioinformatics, NGS, Assembly, DISCOVAR, Variants, BroadInstitute
2935 days ago
Tags: Bioinformatics, NGS, Assembly, Assembler, SPAdes, Reads, Illumina
2934 days ago
Tags: Bioinformatics, Validation, Assembly, BUSCO, Orthologs, NGS
2913 days ago
Tags: Bioinformatics, FASTQ, NGS, ALE, Framework, Stats, Reads, Evaluation, Quality, Assembly
2928 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in fo...Tags: Bioinformatics, FASTQ, NGS, Assembly, Genome, CANU, Assembler, Tool, Software
2911 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organis...Tags: Bioinformatics, NGS, Assembly, Tools, Tutorial, Toolbox
2925 days ago
Tags: Bioinformatics, NGS, Assembly, de novo, Sequence, Assembler, Heterozygous
2911 days ago
Hagfish - assess an assembly through creative use of coverage plots
Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome ...Tags: Bioinformatics, Hagfish, Assess, Assembly, Coverage, Plots, NGS, Structure, Variation, SV, Assembly, Genome
2903 days ago