GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research
GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extract...1984 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from speci...ific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between d...1979 days ago
MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons
MACSE aligns coding NT sequences with respect to their AA translation while allowing N...ted frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a refer...1961 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of obtai...ing an EM algorithm Mining candidate STR alleles from population-scale sequencing data Employing a specialized...1944 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacte...1918 days ago
VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: https://peerj.com/preprints/1895/ Documentation is now hosted on ReadTheDocs1838 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants fro...rom Pacific Biosciences These simulations include sequencing errors, mapping qualities, mu...swift, versatile phylogenomic and high-throughput sequencing simulator https://jackalope....1804 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacte...1824 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. T...loid genomes. A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use...1778 days ago
LRSDAY: Long-read Sequencing Data Analysis for Yeasts
Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism...1772 days ago