All Published Workflows
12 workflows that have been reviewed and published
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
Documentation : https://sanjaynagi.github.io/rna-seq-pop/
Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina
JSON
Sample annotation
Variant calling
genetic variants
snakemake-wrapper-utils
EnhancedVolcano
BCFtools
DESeq2
fastp
FreeBayes
GLUE
HISAT2
kallisto
mosdepth
MultiQC
Pandas
pheatmap
Quant
SAMBLASTER
SAMtools
sleuth
Snakemake
snpEff
Vcflib
data.table
dplyr
ggplot2
ggrepel
jsonlite
openxlsx
RColorBrewer
tidyverse
ipykernel
matplotlib
matplotlib-venn
numpy
papermill
pop-tools
scipy
zarr
Population 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 ...
Ancestral Fasta Generation Workflow for Population Genomics
Introduction
Overview of the two parts of the workflow
Finding query chromosomes homologous to each targ...
Probe: Population Genomic Analysis Workflow for Diploid Organisms
Probe is a snakemake workflow to apply a range of population genomic analyses to whole genome sequencing data, in any diploid...
Evaluating the robustness of polygenic adaptation to the choice of the GWAS cohort
This workflow is built in Snakemake. Please, download Snakemake following the instructions here: https://snakemake.readt...
Partial Reference-Guided Workflow: Gstacks and Pops Analysis
workflow-partial-gstacks-populations These workflows are part of a set designed to work for RAD-seq data on the Galaxy platfo...
Partial Reference-Guided Workflow: BWA-MEM Analysis
workflow-partial-bwa-mem These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using th...
Partial de novo workflow: cstacks-sstacks-gstacks-pops only
workflow-partial-cstacks-sstacks-gstacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy pl...
Partial de novo workflow: ustacks only
workflow-partial-ustacks-only These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, usi...
Stacks RAD-seq de novo workflow
workflow-denovo-stacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using the ...
Stacks RAD-seq reference-guided workflow
workflow-ref-guided-stacks These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using ...
Quality Control of RAD-seq reads on the Galaxy platform
workflow-qc-of-radseq-reads These workflows are part of a set designed to work for RAD-seq data on the Galaxy platform, using...