All Published Workflows

20 workflows that have been reviewed and published

atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
metagem
Show Details View Workflow
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
public

public

Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
JSON raw sequence reads Genome assembly Quality control report prodigal MEGAHIT BWA CheckM fastp kallisto MaxBin memote MetaBAT 2 metaprokka MetaWRAP Quant Roary SAMtools Snakemake SqueezeMeta CONCOCT carve gtdbtk smetana metagenomics
Free
35
covid-19-signal
Show Details View Workflow
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
score-assemblies
Show Details View Workflow
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
ont-assembly-snake
Show Details View Workflow
Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools
public

public

A snakemake-wrapper for easily creating de novo bacterial genome assemblies from Oxford Nanopore (ONT) sequencing data, a...
FASTQ-illumina bacterial Genome assembly Sequence assembly report rasusa BWA CANU Diamond Filtlong Flye Medaka Minimap2 pilon proovframe Racon Raven SAMtools Snakemake Unicycler nanopore
Free
24
ideel
Show Details View Workflow
Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes
public

public

This repo builds on code by Mick Watson who wrote a blog post and follow up about a quick way to test the viabili...
bacterial Genome assembly ORF ID prodigal Diamond Snakemake ggplot2 Genomics
Free
4
trio-assembly-snakemake
Show Details View Workflow
Trio Genome Assembly Snakemake Workflow
public

public

Child reads HiFi in .bam or .fastq.gz Parent reads HiFi in .bam or .fastq.gz Paired en...
Genome assembly Hifiasm SAMtools Snakemake Sequence assembly
Free
9
metagenome-assembly
Show Details View Workflow
Workflow module for metagenome assembly
public

public

A Snakemake workflow for metagenome assembly using metaspades and metahit. It does pre-assembly merging and read-correction i...
Gene ID Sample annotation Genome assembly Quality control report Report prodigal snakemake-wrapper-utils MEGAHIT Pandas SAMtools Snakemake SPAdes TADpole utils metagenomics
Free
19
map_metat
Show Details View Workflow
Snakemake workflow to map and quantify metatranscriptomic data using a metagenome reference
public

public

A Snakemake workflow for mapping metatranscriptomic reads against a metagenomic reference. In short, the workflow maps paired...
FASTQ Sample ID Genome assembly Ontology mapping Bowtie 2 edgeR FeatureCounts metagenomeSeq MultiQC Pandas SAMtools Snakemake metagenomics
Free
15
assembly_10x
Show Details View Workflow
Assembly pipeline for 10X chromium genomes of Mytilus species
public

public

Assembly pipeline from 10x chromium reads from the preprint "Three new genome assemblies of blue mussel lineages: North and S...
GFF JSON Data Genome assembly Sequence assembly report angsd augustus tabix BCFtools BEDTools BUSCO Bwa-mem2 cd-hit fastp GLUE HISAT2 KAT KMC MANTIS Minimap2 mosdepth Nubeam-dedup Pandas RepeatMasker RepeatModeler SAMtools seqkit Snakemake Supernova ggforce ggplot2 scales defopt numpy Trim_Galore Sequence assembly
Free
112
nanoplasm
Show Details View Workflow
NanoPlasm
public

public

v1.0 NanoPlasm is a specialized workflow designed for the purpose of assembling, typing, and analyzing plasmid sequences usin...
raw sequence reads Genome assembly Plot nanofilt Biopython BWA fastp FastQC Flye Medaka Pandas Snakemake Unicycler Genomics
Free
18
mag
Show Details View Workflow
Assembly and binning of metagenomes
public

public

nf-core/mag is a bioinformatics best-practise analysis pipeline for assembly, binning and annotation of metagenomes. The p...
Genome assembly augustus bioawk gunc porechop prodigal pydamage MEGAHIT AdapterRemoval BCFtools Biopython Bowtie 2 BUSCO CAT Centrifuge CheckM Consensus DAS fastp FastQC Filtlong FreeBayes kraken2 Krona MetaBAT 2 metaprokka metaspades MultiQC NanoPack NanoPlot Nextflow Pandas SAMtools SqueezeMeta CONCOCT gtdbtk Sequence assembly
Free
81