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/s12864-017-3927-82249 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...2244 days ago
MITObim - mitochondrial baiting and iterative mapping
This document contains instructions on how to use the MITObim pipeline described in...inciple also data from the Iontorrent, 454 and PacBio sequencing platforms. Below you can fin...2241 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 (both DNA and RNA) to a...strategies, enable rapid and accurate alignment of sequencing reads. This new indexing sche...2241 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...2220 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignme...netic dissimilarity which operates upon raw sequ...d without assembling one. De novo estimates of genetic relatedness from next-gen sequencing data https://kwip.readthedocs...2220 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.... 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...2218 days ago
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PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a...ements for genome assembly: PRICE uses paired-read information to iterati...individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non...2207 days ago