All Published Workflows
7 workflows that have been reviewed and published
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakema...
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
BGCFlow is a systematic workflow for the analysis of biosynthetic gene clusters across large collections of genomes (p...
JSON
CleanEx dataset code
Clustering
Text mining report
bigslice
refseq_masher
antiSMASH
Biopython
cblaster
CheckM
Diamond
eggNOG-mapper v2
FastANI
metaprokka
MLST
Pandas
Peppy
Roary
seqfu
Snakemake
alive-progress
gtdbtk
matplotlib
ncbi-genome-download
networkx
numpy
plotly
PyYAML
requests
Comparative genomics
Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
John Huddleston1,2, John R. Barnes3, Thomas Rowe3, Xiyan Xu3, Rebecca Kondor3, David E. Wentworth3, Lynne Whittaker4, Burcu ...
Hi-C and region capture Hi-C Workflows
This can also be used for Hi-ChIP experiments, in that case the output with matrix with iced values is ignored and the matr...
CUT&RUN (and CUT&TAG) Workflow
The workflow needs a single input which is a list of dataset pairs of fastqsanger.
adapter sequences: this depends o...
ChIP-seq paired-end Pipeline
ChIP-seq paired-end Workflow
The workflow needs a single input which is a list of dataset pairs of fastqsanger.
adapt...
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...