RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institute and the Hebrew University of Je...ly to process large volumes of RNA-seq reads. Trinity partitions the sequ...n). Chrysalis then partitions the full read set among these disjoint grap...like so: Trinity --seqType fq --left reads...2960 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. It is fully parallelized and can run...ory. PEAR evaluates all possible paired-end read overlaps and without requirin...ntation, it can merge millions of paired end reads...2946 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 reference genome fo...put an assembly in FASTA format and paired reads mapped to the assembly in a...-assemblies. REAPR works best using mapped read...2946 days ago
2937 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_reve...or N bases (below quality 3) (TRAILING:3) Scan the read with a 4-base wide sliding wi...per base drops below 15 (SLIDINGWINDOW:4:15) Drop reads...2937 days ago
2927 days ago
2926 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...n and segmental duplications. mrFAST maps short reads with respect to user defined...nd 'all' mappings for a given set of reads...2926 days ago
CANU: Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.
Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the P...ce consensus Trim corrected sequences Assemble trimmed corrected sequences Read...2909 days ago
2912 days ago