3007 days ago
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
...ew kilobytes of memory. PEAR evaluates all possible paired-end read overlaps and without requiring the ta...p computer. More at http://www.exelixis-lab.org/web/software/pear Paper: http://www.ncbi.nlm.n...3007 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 reads, without...embly in FASTA format and paired reads mapped to the assembly in a BAM f...is analysed to locate mis-assemblies. REAPR works best using mapped read...3007 days ago
2998 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
...se_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 This will perform the following: Remove adapters (ILLUMINACLIP:TruSeq3-PE....2998 days ago
HOMER: Software for motif discovery and next-gen sequencing analysis
...eving and storing sequencing files (your own data or from public sources) Checking sequence quality, trimming, general sequence manipulation Mapping reads to a reference geno...2987 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 specia...variation and segmental duplications. mrFAST maps short reads with respect to...mrFAST is designed to find 'all' mappings for a given set of reads...2987 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
...el free to use and report issues encountered. Canu is a hierachical assembly pipeline which runs in four steps: Detect overlaps in high-noise sequences using MHAP Generate corrected sequence...2970 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
...aim of the research is to know where the large-scale [chromosomal by chromosome] of several primates was equal/different, having at a glance a map of the entire genomes.2987 days ago
RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008...to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool...2986 days ago