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...cific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between d...1977 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...nted frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a refer...1959 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...sing an EM algorithm Mining candidate STR alleles from population-scale sequencing data Employing a specialized...1942 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 bact...1916 days ago
HumCFS: a database of fragile sites in human chromosomes
Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosd...S, which provides comprehensive information about experimentally identified CFS at a single sou...1897 days ago
MGERT: Mobile Genetic Elements Retrieving Tool
MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different technical quirks from an inexperienced user.1870 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
jackalope simply and efficiently simulates (i) variants from reference ge...fluctuations. jackalope can simulate single,...iosciences These simulations include sequencing errors, mapping qualities, mu...ile phylogenomic and high-throughput sequencing simulator https://jackalope....1801 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 bact...1821 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitb...N50 values in the range of dozens of Mb and pseudomolecules with better gene space repre...col for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use...1776 days ago
Miropeats: discovers regions of sequence similarity amongst any set of DNA sequences
Miropeats discovers regions of sequence similarity amongst any set of DNA sequences and then...sequence similarity by summarizing extensive large scale sequence similarities on a single pag...1770 days ago