All Published Workflows

4 workflows that have been reviewed and published

snakemake_haps
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A snakemake workflow for high-throughput amplicon sequencing
public

public

This is a snakemake workflow for generating a list of variants (Single Nucleotide Polymorphisms- SNPs) from amplicon sequenci...
Haplotype map Haplotype mapping Quality control report tabix BCFtools BEDTools BWA FastQC FreeBayes MultiQC pyfasta QualiMap SAMtools Snakemake Trimmomatic VCFtools Polymorphisms
Free
8
octo_snakemake
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workflow for hifiasm assembly stuff
public

public

workflow for hifiasm assembly stuff Hifiasm is used for assembling DNA sequences. It was originally developed for assembling ...
raw sequence reads Haplotype mapping Haplotype map assembly-stats Hifiasm Snakemake De Novo
Free
3
coredupgraph
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Defining Paralogy Relationships among Haplotype Core Duplicons
public

public

Pipeline relating haplotype core duplicons to each other to define paralogy. This is a Snakemake project template. The Snak...
Haplotype mapping BEDTools Minimap2 SAMtools Snakemake Sequence analysis
Free
1
haplotype_calling_pipeline
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Running the haplotype/variant calling pipeline with Snakemake
public

public

Overview: Using samples from amplicon deep sequencing from gene targets, either call haplotypes or call variants. Method: Tar...
FASTQ raw sequence reads Haplotype mapping Variant calling genetic variants MultiQC Snakemake gene similarity analysis
Free
16