All Published Workflows

81 workflows that have been reviewed and published

kraken2_classification
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Snakemake workflow for metagenomic classification with Kraken2
public

public

A Snakemake pipeline wrapper of the Kraken2 short read metagenomic classification software, with additional tools for analysi...
Database ID Taxonomic classification Plot bracken kraken-biom cmapR ALDEx2 Kraken kraken2 Krona Pandas Snakemake ggplot2 ggpubr RColorBrewer reshape2 vegan metagenomics
Free
18
struo
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Ley Lab MetaGenome Profiler DataBase generator
public

public

Struo: a pipeline for building custom databases for common metagenome profilers "Struo" --> from the Latin: “I build” or...
bracken prodigal Bowtie 2 Diamond kraken2 Snakemake VSEARCH
Free
17
phanta
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Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
public

public

Workflow figure created on BioRender.com. Pinto, Y., Chakraborty, M., Jain, N. et al. Phage-inclusive profiling of human gut ...
bacterial Labeled quantification Scatter plot plotting Plot bracken kraken2 Pandas Snakemake stringr numpy metagenomics
Free
23
covid-19-signal
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Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
public

public

This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing. This core work...
FASTQ-illumina Query script Genome assembly Taxonomic classification tabix BCFtools BEDTools breseq BWA Consensus FastQC FreeBayes iVar kraken2 Pangolin QUAST SAMtools Snakemake vt Trim_Galore COVID19 Risk Mitigation
Free
31
stag-mwc
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StaG Metagenomic Workflow Collaboration
public

public

The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing a metagenomics analysis workflow suitable for ...
JSON bracken BBMap Bowtie 2 fastp FeatureCounts humann Kaiju Kraken kraken2 KrakenUniq Krona MetaPhlAn MultiQC Pandas SAMtools Singularity Hub Snakemake matplotlib numpy seaborn
Free
78
metax_bakeoff_2019
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Metagenomic Taxonomic Classification Benchmarking Workflow
public

public

Metagenomic taxonomic classification benchmarking This package is contains snakemake workflows, a jupyter notebook and a pyth...
raw sequence reads Taxonomic classification Taxonomy bracken prophyle BLAST Centrifuge Diamond FastQC Kaiju Kraken kraken2 metaX Picard SAMtools seqtk Snakemake ncbi-genome-download metagenomics
Free
78
nbis-meta
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A snakemake workflow for metagenomic projects
public

public

A workflow for metagenomic projects A snakemake workflow for paired- and/or single-end whole-genome shotgun metagenomic d...
Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI
Free
137
rna-seek
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A comprehensive quality-control and quantification RNA-seq pipeline
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public

An open-source, reproducible, and scalable solution for analyzing RNA-seq data. Introduction Overview 2.1 R...
preseq Arriba Bowtie 2 Cutadapt FastQC kraken2 Krona MultiQC Picard QualiMap RSEM SAMtools Snakemake STAR
Free
41
ccbr_gatk4_exome_seq_pipeline
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An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH
public

public

GATK4 Whole Exome-sequencing Pipeline . This is the home of the pipeline, exome-seek. Its long-term goals: to accura...
gatk sequenza-utils BCFtools Bowtie 2 BWA FastQC illumina kraken2 Krona MultiQC Picard QualiMap SAMBLASTER SAMtools Snakemake Trimmomatic VarScan VCFtools MuTect
Free
63
pipelord
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A microbial genomic analysis pipeline used by the Djordjevic Lab
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public

This repo contains a genomic analysis pipeline used for analysing mostly E. coli genomes, though it also sees use in anal...
ABRicate AMRFinderPlus abritamr assembly-stats bracken Bakta BLAST DFAST fastp IQ-TREE KMA kraken2 metaprokka MLST MOB-suite Pandas Roary shovill Snakemake
Free
74
on-rep-seq
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Bulk Typing of Bacterial Species down to Strain Level
public

public

ON-rep-seq is a molecular method where bacterial (or yeast) selective intragenomic fragments generated with Rep-PCR are seque...
porechop CANU Cutadapt kraken2 Snakemake VSEARCH matplotlib numpy
Free
12
methyl-seek
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Bisulphite-sequencing based methylation pipeline
public

public

Bisulphite-sequencing methylation pipeline . This is the home of the pipeline, methyl-seek. Its long-term goals: to ...
BEDTools Bowtie 2 FastQC homer Kraken kraken2 Krona MultiQC Picard SAMtools Singularity Hub Snakemake Bismark Trim_Galore
Free
31