All Published Workflows
9 workflows that have been reviewed and published
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
A snakemake-wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, a...
Assembly pipeline for 10X chromium genomes of Mytilus species
Assembly pipeline from 10x chromium reads from the preprint
"Three new genome assemblies of blue mussel lineages: North and S...
GFF
JSON
Data
Genome assembly
Sequence assembly report
angsd
augustus
tabix
BCFtools
BEDTools
BUSCO
Bwa-mem2
cd-hit
fastp
GLUE
HISAT2
KAT
KMC
MANTIS
Minimap2
mosdepth
Nubeam-dedup
Pandas
RepeatMasker
RepeatModeler
SAMtools
seqkit
Snakemake
Supernova
ggforce
ggplot2
scales
defopt
numpy
Trim_Galore
Sequence assembly
Assemblosis: CWL based workflow to assemble haploid/diploid eukaryote genomes of non-model organisms
The workflow is designed to use both PacBio long-reads and Illumina short-reads. The workflow first extracts, corrects, trims...
VGP HiFi phased assembly with hifiasm and HiC data workflow
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
VGP hybrid scaffolding with HiC data
Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly co...
VGP HiFi phased assembly with hifiasm and HiC data
Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.
Trinity RNA Assembly pipeline
The pipeline requires Nextflow to run.
DSL2 syntax is used, so that Nextflow version 20.07.1 or higher is required.
NOTE...
Indices builder from GBOL RDF (TTL)
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (ann...