1987 days ago
NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads
NxRepair is a python module that automatically detects large structural...in de novo assemblies using Nextera mate pair reads. The decector will brea...ct, unaffected contigs. https://nxrepair.readthedocs.io/en/latest/tuto...ml nxrepair aligned_matepairs....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 species, wh...ic ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between d...1978 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 allowin...ented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a refer...1960 days ago
HipSTR: Haplotype inference and phasing for Short Tandem Repeats
HipSTR was specifically developed to deal with these errors in the hopes of ob...using 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 bacte...1916 days ago
jackalope: A swift, versatile phylogenomic and high-throughput sequencing simulator
...ctuations. jackalope can simulate single, paired-end, or mate-pair Illumina reads, as well as re...fic Biosciences These simulations include sequencing errors, mapping qualities, mu...ersatile phylogenomic and high-throughput sequencing simulator https://jackalope....1802 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...1822 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidde...1818 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository....yploid genomes. A protocol for generating chromosome-conformation capture sequencing (Hi-C) data suitable for use...1776 days ago