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.1811 days ago
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants.1742 days ago
Flye: Fast and accurate de novo assembler for single molecule sequencing reads
...It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads...1762 days ago
dnaPipeTE: a pipeline designed to find, annotate and quantify Transposable Elements
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is ver...1724 days ago
TRITEX sequence assembly pipeline for Triticeae genomes
The pipeline is open-source and hosted in a public Bitbucket repository. TRITEX...mosome-conformation capture sequencing (Hi-C) data suitable for use with the pipeline is described in Himmelba...1717 days ago
1705 days ago
RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
...wing features: Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minu...1649 days ago
HaploTypo: a variant-calling pipeline for phased genomes
...nomes are available. However, most genetic variant calling tools do not explicitly account for haplotype structure. Here, we present HaploTypo, a pipeline tailored to resolve haplotype...1596 days ago
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performan...1560 days ago
1558 days ago