2940 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/pandaseq2963 days ago
RACA: Reference-Assisted Chromosome Assembly
Rreference-Assisted Chromosome Assembly (RACA), an algorithm to reliably order and orient sequence scaffolds gen...o longer chromosomal fragments using comparative genome information and paired-end reads...2963 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...f memory. PEAR evaluates all possible paired-end read overlaps and without req...plementation, it can merge millions of paired end reads...2963 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 can be used in any stage of an assembly pipe...2962 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.gz output_reverse_...2954 days ago
2943 days ago
2926 days ago
Hagfish - assess an assembly through creative use of coverage plots
Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (...ish requires a reference sequence and a paired end re-sequencing data set....more power the larger the insert size of the paired end libra...2918 days ago
2886 days ago