3007 days ago
RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institut...cess large volumes of RNA-seq reads. Trinity partitions the sequ...alis then partitions the full read set among these disjoint grap...cing the paths that reads and pairs of reads take within the gra...Trinity --seqType fq --left reads_1.fq --right reads_2.fq --CPU...2979 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...2965 days ago
REAPR: a universal tool for genome assembly evaluation
REAPR is a tool that evaluates the accuracy of...ome assembly using mapped paired end reads, without the use of a refere...assembly in FASTA format and paired reads mapped to the assembly in a...blies. REAPR works best using mapped read pairs from a large insert library (...2965 days ago
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_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...2956 days ago
2946 days ago
2945 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...2945 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...2928 days ago