All Published Workflows

76 workflows that have been reviewed and published

score-assemblies
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Score and compare multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s)
public

public

A snakemake-wrapper for evaluating de novo bacterial genome assemblies, e.g. from Oxford Nanopore (ONT) or Illumina seque...
bacterial Genome assembly Genome report nucdiff prodigal Bakta BUSCO Diamond Minimap2 QUAST SAMtools seqkit Snakemake ggplot2 tidyverse Comparative genomics nanopore
Free
32
ncov-recombinant
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Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
public

public

❗❗❗ Note : ncov-recombinant will be deprecated soon as SARS-CoV-2 recombination has evolved beyond the scope of this pip...
JSON csvtk nextclade Biopython CLICK Pandas Pangolin seqkit Snakemake epiweeks functions matplotlib numpy pango-aliasor PyYAML requests
Free
29
hamronization_workflow
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Harmonization of AMR predictor tool outputs
public

public

hAMRonization is a project aiming at the harmonization of output file formats of antimicrobial resistance detection tools. Th...
ABRicate AMRFinderPlus ariba prodigal srst2 BLAST BWA GROOT hmmsearch (genouest) KMA SAMtools seqkit Snakemake sraX Trimmomatic DeepARG v2.0 hAMRonization oschmod RGI
Free
49
kgwasflow
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kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
public

public

A modular, flexible, and reproducible Snakemake workflow to perform k-mers-based GWAS. Summary Installation ...
snakemake-wrapper-utils tabix BEDTools BLAST Bowtie 2 Cutadapt FastQC KMC Minimap2 MultiQC Pandas SAMtools seqkit Snakemake SPAdes matplotlib natsort numpy pysam qmplot scipy seaborn
Free
85
dtr-phage-pipeline
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"DTR Phage Genome Polishing Pipeline"
public

public

DTR phage pipeline The DTR phage pipeline is a Snakemake pipeline for obtaining polished, full-length dsDNA bacteriophage gen...
raw sequence reads Sequence read processing Genome report mummer2circos porechop prodigal Kaiju Krona Medaka Minimap2 seqkit Snakemake matplotlib Genomics
Free
51
vgea
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VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.
public

public

VGEA (Viral Genomes Easily Analyzed) is an RNA viral assembly toolkit. VGEA was developed to aid in the analysis of next gene...
BWA fastp MultiQC QUAST SAMtools seqkit Snakemake
Free
12
viralmetagenomicspipeline
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Pipeline for metagenomic community analysis using DNA isolated from virus-like particles
public

public

This repo can be used to generate all of the desired output files for community analysis (shared OTUs, taxonomies, alpha/beta...
r-virfinder bam_to_sam_parallel BBMap BCFtools bcf-tools-cat bcf-tools-index Bowtie 2 BWA-SW CAT and BAT cloudSPAdes mbwa_wrapper metaspades plasmidspades QUAST rnaspades sam_to_bam SAMtools samtools_flagstat samtools_idxstats samtools_slice_bam samtools_sort seqkit Snakemake SPAdes Trimmomatic
Free
45
monkeypox
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Nextstrain build for mpox virus
public

public

This is the Nextstrain build for MPXV (mpox virus). Output from this build is visible at nextstrain.org/monkeypox . T...
JSON nextclade treetime Augur Biopython Pandas seqkit Snakemake TreeTime
Free
38
acastellanii_genome_analysis
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Comparative analysis of the genomes from two Acanthamoeba castellanii strains
public

public

This repository contains scripts and documentation related to the analysis and comparison of the Acanthamoeba castellanii ...
assembly-stats cooler BEDTools Biopython BLAST BUSCO cd-hit Diamond genomepy MaxBin Minimap2 NG-Circos OrthoFinder Pandas patcHwork QUAST seqkit Snakemake topGO dplyr ggplot2 gridExtra readr stringr tibble tidyr tidyverse viridis cooler matplotlib matplotlib-venn numpy reportlab seaborn
Free
57
meclip
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Snakemake based analysis pipeline to identify m6As from eCLIP data
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public

meCLIP is method to identify m6As residues at single-nucleotide resolution using eCLIP. It uses the Snakemake workflow manage...
umi_tools BEDTools Cutadapt FastQC GFFutils gtftogenepred MultiQC SAMtools seqkit Snakemake STAR subSeq scales
Free
23
polyaterminus
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Polyadenylation aware read trimming and alternative polyadenylation site analysis
public

public

Purpose of the work flow is to run RNA-seq trimming and alignment to a given reference steps and perform initial polyadenylat...
BBMap FastQC MultiQC Sambamba seqkit Snakemake STAR
Free
26
phage-evo-paper
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Repository to store the analysis of the paper on phage evolution.
public

public

A Snakemake workflow for Phage directed evolution analysis .
Data index Analysis Report FastANI MMseqs NanoPlot SAMtools seqkit Snakemake Molecular evolution
Free
12