QUAST: quality assessment tool for genome assemblies
QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with and without a given reference genome.The tool accepts multiple assemblies,...2964 days ago
REAPR: a universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end rea...n order to score each base of the assembly. http://www.sanger.ac.uk/science/tools/reapr2964 days ago
2956 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Paired End: java -jar trimmomatic-0.35.jar PE -phred33 input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_revers...2956 days ago
mrFAST: Micro Read Fast Alignment Search Tool
mrFAST is a read mapper that is designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplicat...2945 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
Smash is a completely alignment-free method/tool to find and visualise genomic rearrangements. The detection is based on conditional exclusive compression, namely using a FCM (Markov m...2944 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotat...ently, in order to make RAST a more useful research tool and to keep pace with advance...and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular versi...2944 days ago
YASS :: genomic similarity search tool
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or p...most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BL...them to local alignments. This genomic search tool uses multiple transition cons...2939 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 (am...2920 days ago
RCircos: an R package for Circos 2D track plots
RCircos package provides a simple and flexible way to make Circos 2D track plots with R a...ng large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos im...2921 days ago