RACA: Reference-Assisted Chromosome Assembly
...rder and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. http://www.ncbi.nlm.nih.gov...2963 days ago
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger...her with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on...2962 days ago
QUAST: quality assessment tool for genome assemblies
QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project.It can works both with...ioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long2962 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 the use of a referen...res as input an assembly in FASTA format and paired reads mapped to the assembly in a B...2962 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
...Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15) Drop reads below the 36 bases long (MINLEN:36) More at http://...2954 days ago
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HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which i...s) Checking sequence quality, trimming, general sequence manipulation Mapping reads to a reference genome Manipu...2943 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 emphasi...segmental duplications. mrFAST maps short reads with respect to user defined...sp;'all' mappings for a given set of reads, however it can return one "b...2943 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highl...sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of...2941 days ago