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...es as input an assembly in FASTA format and paired reads mapped to the assembly in a B...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_revers...g when the average quality per base drops below 15 (SLIDINGWINDOW:4:15) Drop reads below the 36 bases long (MINL...2948 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 is im...Checking sequence quality, trimming, general sequence manipulation Mapping reads to a reference genome Manipu...2937 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...2937 days ago
GATB : Genome Analysis Toolbox with de-Bruijn graph
The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly ef...ts of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of...2935 days ago
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