MITObim - mitochondrial baiting and iterative mapping
...ssembler, MITObim supports in principle also data from the Iontorrent, 454 and PacBio sequencing platforms. Below you can find a few basic tutorials for how...2188 days ago
Metassembler: merging and optimizing de novo genome assemblies
...nsensus assembly using the best segments of the individual assemblies. Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, alt...2188 days ago
Porechop: tool for finding and removing adapters from Oxford Nanopore reads
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends...into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequenc...2167 days ago
2165 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatM...ser-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all2161 days ago
Many-to-many pairwise alignments of two sequence sets
...alignments to file. It uses the Needleman-Wunsch alignment algorithm to find the optimum alignment (includ...ontains values for every possible residue or nucleotide match. Needleall finds the alignment with the maxim...2146 days ago
ReMILO: reference assisted misassembly detection algorithm using short and long reads.
...a structure called red-black multipositional de Bruijn graph to detect misassemblies. In addition, ReMILO also aligns the contigs to long reads and find their differences from the lo...2129 days ago
Instructions for Creating Your Own R Package
The following is a step-by-step guide to creating your own R package. Even beyond this course, youmay find this useful for storing functions you create for your own research or...1536 days ago
Snippy: Rapid haploid variant calling and core SNP phylogeny
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and...2024 days ago
CoLoRMap: Correcting Long Reads by Mapping short reads
...ality Illumina paired-end reads mapped onto the long reads. Our algorithm is based on two novel ideas: using a classical shortest path algorithm to find a sequence of overlapping sho...2083 days ago