NGMLR: long-read mapper designed to align PacBio or Oxford Nanopore
CoNvex Gap-cost alignMents for Long Reads (ngmlr) is a long-read mapper designed t...as designed to quickly and correctly align the reads, including those spanning (co...ns. The k-mer search helps to detect and split reads that cannot be aligned linear...2207 days ago
ALPACA: A hybrid strategy for assembly of genomic DNA shotgun sequencing reads.
ALPACA requires Celera Assembler 8.3 or later. It is recommended to build Celera Assembler from source. (Why? The pre-built binaries CA_8.3rc1 and CA8.3rc2 will work for any large data set. Detail paper at https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3927-82202 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore...gies. The algorithm uses an A-Bruijn graph to find the overlaps between reads and does not require them to...2197 days ago
2197 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...expressed transcripts. Scallop achieves this improvement through a novel algorithm that can be proved preserving all phasing paths from reads and paired-end reads, while also achieves both tra...2194 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
...and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a popul...alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is...2194 days ago
Porechop: tool for finding and removing adapters from Oxford Nanopore reads
...s a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a r...its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough a...2173 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
...hted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the...2173 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
...sequencing data can be used for the assembly and for the mapping of the reads. A full documentation on the...is available here. We recommend BWA for mapping of the reads. When the mapping has been p...2172 days ago
Ranbow: a haplotype assembler for polyploid genomes
...w has three main modes of function: ranbow hap: for haplotyping ranbow eval: for evaluating of the assemble haplotypes by gold standard (long) reads ranbow phylo: for the phylo...2170 days ago