3045 days ago
RNA-Seq De novo Assembly Using Trinity
Trinity, developed at the Broad Institute and the Hebrew University of J...y to process large volumes of RNA-seq reads. Trinity partitions the sequ...). Chrysalis then partitions the full read set among these disjoint grap...ike so: Trinity --seqType fq --left reads_1.fq...3018 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 ru...ry. PEAR evaluates all possible paired-end read overlaps and without requirin...tation, it can merge millions of paired end reads with...3003 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 f...ut an assembly in FASTA format and paired reads mapped to the assembly in a...assemblies. REAPR works best using mapped read pairs...3003 days ago
2995 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 belo...2995 days ago
2984 days ago
2984 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, how...2984 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 PacBio RSII or Oxford Nanopore Min...sequences Assemble trimmed corrected sequences Read the&n...2967 days ago