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/reapr2948 days ago
2940 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...2940 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...2929 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 (M...2928 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
...their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advance...is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular versi...2927 days ago
YASS :: genomic similarity search tool
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta...most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BL...d them to local alignments. This genomic search tool uses multiple transition cons...2922 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...2904 days ago
RCircos: an R package for Circos 2D track plots
...her R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos im...2904 days ago
Bpipe - a tool for running and managing bioinformatics pipelines
...ling List (Google Group) Bpipe has been published in Bioinformatics! If you use Bpipe, please cite: Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioi...2903 days ago