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 to se...ompute precise alignments. The gap model allows ngmlr to account for both the sequencing error and real genomic variat...2251 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/s12864-017-3927-82246 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 Technologies. The algorithm uses an A-Bruijn graph to find the...2242 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in Ha...nciple also data from the Iontorrent, 454 and PacBio sequencing platforms. Below you can fin...2238 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (b...lation of human genomes (as well as to a single reference genome). Based on an ex..., enable rapid and accurate alignment of sequencing reads. This new indexing sche...2238 days ago
Metassembler: merging and optimizing de novo genome assemblies
Metassembler combines multiple whole genome de novo assemblies into a combined consensus ass...cally run multiple algorithms in an attempt to find the single b...ithm that merges multiple assemblies of a genome into a single sup...2238 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 of reads are trimmed off, and when a read has an adapter in its midd...2217 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implement...ple genetic dissimilarity which operates upon raw sequencing reads. It is able to calculat...vo estimates of genetic relatedness from next-gen sequencing data https://kwip.readthedocs...2217 days ago
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
SEX-DETector is a probabilistic method that relies on RNAseq data from a cr...How does SEX-DETector work? SEX-DETector does not require prior sequencing of a reference genome: the same sequencing data can be used for the asse...2216 days ago
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