All Published Workflows

50 workflows that have been reviewed and published

snakemake_anvio
Show Details View Workflow
Anvi'o Analysis Workflow Using Snakemake
public

public

snakemake rules for running anvio This Snakefile will run a basic anvi'o analysis of a set of assemblies and a set of sam...
Sequence assembly Analysis Data Anvio Bowtie 2 Centrifuge SAMtools Snakemake Sequence analysis Sequence assembly
Free
12
yaatap
Show Details View Workflow
Automated Transcript Assembly Pipeline with Dependencies
public

public

yetAnotherAutoTranscriptAssemblyPipeline ffq v0.2.1 FastQC v0.11.8 BBDuk v35.85 Kraken2 v2.1.2 ContFree-N...
Quant Snakemake Sequence assembly
Free
19
mgi-ncov19-snakemake
Show Details View Workflow
mgi-ncov19 Snakemake COVID-19 Analysis Pipeline with Classification and De Novo Assembly
public

public

This snakemake pipeline can conduct cov-19 virus classification, de novo assembly, coverage assessment and variant calling. T...
BWA fastp kraken2 Picard SAMtools Snakemake SOAPnuke SPAdes Sequence assembly
Free
8
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
snakemake-hisat2-stringtie
Show Details View Workflow
Snakemake Workflow: De Novo Transcriptome Assembly with HISAT2 and StringTie
public

public

Snakemake workflow: De novo transcriptome assembly with Hisat2 and StringTie. This pipeline comprises all steps of the 'new t...
DeepTools FastQC gffcompare MultiQC Sambamba SAMtools Snakemake StringTie Trimmomatic Sequence assembly
Free
24
miseq_bac_assembly_annot_workflow
Show Details View Workflow
Bacterial Genome Assembly with Snakemake Workflow
public

public

This is the template for a new Snakemake workflow. Replace this text with a comprehensive description covering the purpose an...
skesa metaprokka Pandas QUAST seqkit Snakemake SPAdes Trim_Galore Sequence assembly
Free
7
repairnatrix
Show Details View Workflow
RepairNatrix - An example workflow
public

public

*DAG of an example workflow for RepairNatrix
JSON Biopython BLAST Pandas PANDAseq seqtk Snakemake SPAdes VSEARCH constraints dinopy kMer numpy PyYAML tqdm fastDNA Sequence assembly
Free
26
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
hi-c-scaffolding
Show Details View Workflow
Hi-C Scaffold Assembly Workflow with Snakemake
public

public

A snakemake workflow that scaffold assembly using Hi-C data snakemake --cores [cpu] --use-conda
BWA Picard SAMtools Snakemake YaHS Sequence assembly
Free
11
chimerenanoporepipeline
Show Details View Workflow
Snakemake workflow: ChimereNanoporePipeline
public

public

A snakemake workflow that takes fastq files as input and creates a mitochondrial genome assembly. As mentioned the workflow i...
Chimera detection Bandage Biopython Diamond MITOS Pandas Porechop_ABI seqkit seqtk Snakemake SPAdes subSeq fastq matplotlib numpy SACRA Sequence assembly
Free
17
metatdenovo
Show Details View Workflow
Assembly and annotation of metatranscriptomic data
public

public

nf-core/metatdenovo is a bioinformatics best-practice analysis pipeline for Assembly and annotation of metatranscriptomic ...
Sequence annotation bioawk prodigal MEGAHIT BBMap CAT Diamond eggNOG-mapper v2 FastQC FeatureCounts hmmsearch (genouest) metaprokka MultiQC Nextflow SAMtools seqtk SPAdes TransDecoder data.table dplyr dtplyr purrr readr stringr tidyr tidyverse EUKulele kofam_scan Trim_Galore Sequence assembly
Free
54
genomeskim
Show Details View Workflow
QC and filtering of genome skims, followed by organelle assembly and/or genome analysis
public

public

nf-core/genomeskim is a bioinformatics best-practice analysis pipeline for QC and filtering of genome skims, followed by o...
FastQC MultiQC Nextflow Data quality management Sequence assembly Whole genome sequencing
Free
4