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
...ably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. http://www.ncb...2965 days ago
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
...ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully...lobytes of memory. PEAR evaluates all possible paired-end read overlaps and with...imized implementation, it can merge millions of paired end reads within a couple...2965 days ago
REAPR: a universal tool for genome assembly evaluation
...the accuracy of a genome assembly using mapped paired end reads, without the use...quires as input an assembly in FASTA format and paired reads mapped to the assemb...-assemblies. REAPR works best using mapped read pairs from a large insert library...2965 days ago
Trimmomatic: A flexible read trimming tool for Illumina NGS data
Paired End: java -jar trimmomatic-0.35.jar PE -phr...rward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paire...N bases (below quality 3) (LEADING:3) Remove trailing low quality or N bases (b...2956 days ago
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 Oxford Nanopore MinION). The software...2928 days ago
Smash: An alignment-free method to find and visualise rearrangements between pairs of DNA sequences
...lues (only value varies). The method can perform both in small- and large-scale. Nevertheless is more directed to large-scale since that the main aim of the research is to k...2945 days ago
2931 days ago