2942 days ago
PAired-eND Assembler for DNA sequences
PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. More at https://github.com/neufeld/pandaseq2965 days ago
2965 days ago
RACA: Reference-Assisted Chromosome Assembly
Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds gen...into longer chromosomal fragments using comparative genome information and paired-end reads....2965 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...es of memory. PEAR evaluates all possible paired-end read overlaps and without req...d implementation, it can merge millions of paired end reads...2964 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 for comparison. It...The software requires as input an assembly in FASTA format and paired rea...2964 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_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq....2956 days ago
2945 days ago
HOMER: Software for motif discovery and next-gen sequencing analysis
This tutorial covers topics independently of HOMER, and represents knowledge which is important to know bef...OMER. Setting up your computing environment Retrieving and storing sequencing files (your own data or...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 PacBio RSII or O...2928 days ago