All Published Workflows
11 workflows that have been reviewed and published
Snakemake workflow to download and/or align reads to targets and produce useful outputs.
A Snakemake workflow to download/align reads to targets and produce useful outputs. With hiss, you can:
Download reads fo...
Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection
Fastq to bam mapping pipeline with marked duplicates, indexing, and insert size metric collection This is a Snakemake-based p...
Barcode Mapping and Read Extraction Workflow with bcmap
Maps barcodes to a reference genome and returns genomic windows from which the barcoded reads most likely originate. Each win...
Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows
Snakemake implementation of data pre-processing for variant discovery from GATK Best Practices Workflows
Coprolite host Identification pipeline
CoproID helps you to identify the "true maker" of Illumina sequenced Coprolites/Paleofaeces by checking the microbiome...
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
nf-core/isoseq is a bioinformatics best-practice analysis pipeline for Isoseq gene annotation with uLTRA and TAMA. Startin...
Pox Virus Illumina Amplicon Workflow for half-genomes sequencing data
This workflow generates consensus sequences from Illumina PE-sequenced ARTIC data of pox virus samples.
It requires that all ...
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...
BridgeDb workflow: Gene HGNC name to Ensembl identifier
This tutorial explains how to use the BridgeDb identifier mapping service to translate HGNC names to Ensembl identifiers. Thi...
GATK-Variant Calling Pipeline
Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect ...
Plant virus confirmation
Mapping against all plant virus then make contig out of the mapped reads then blast them..