All Published Workflows

7 workflows that have been reviewed and published

foodme
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A reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special focus on food and feed samples.
public

public

FooDMe is a reproducible and scalable snakemake workflow for the analysis of DNA metabarcoding experiments, with a special fo...
JSON paired sequencing data Filtering Quality control report Biopython BLAST Consensus Cutadapt fastp Krona Pandas seqtk Snakemake DT htmltools tidyverse PyYAML taxidTools Taxonomy
Free
60
snake_hisat_cutadapt
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Snakemake Pipeline for Paired-End RNA-Seq Data Analysis
public

public

snakemake_PE_RNAseq This pepeline is inspired by crazyhottommy . test generate workflow plot snakemake --dag 2> /dev/null...
paired sequencing data ballgown Cutadapt DeepTools FastQC MultiQC SAMtools Snakemake magrittr RNA-Seq
Free
10
analysis_of_multi_way_chromatin_interactions_from_
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Analysis of multi-way chromatin interactions from very long sequencing reads
public

public

The thesis is focused on the concept of “chromosomal walks” introduced by Olivares-Chauvet et al., 2016. These chromosomal wa...
TSV paired sequencing data Expression analysis Filtering Plot BEDTools Biopython Bowtie 2 Pandas SAMtools Snakemake intervaltree matplotlib networkx numpy pysam scipy seaborn De Novo
Free
17
smk_emseq
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SnakeMake workflow for the processing of EMseq data
public

public

paired sequencing data Sequencing quality control Quality control report BBMap FastQC SAMtools Snakemake Bismark Data mining
Free
9
scrnaseq-single-sample-processing-starsolo
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scRNAseq Single Sample Processing STARSolo
public

public

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do...
FASTQ paired sequencing data Clustering Gene expression matrix Sample annotation ANN-SoLo Galaxy SCANPY WorkflowHub scRNAseq data processing
Free
eukrecover
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EukRecover: Pipeline to recover eukaryotic MAGs using CONCOCT, metaBAT2 and EukCC's merging algorythm.
public

public

EukRecover Pipeline to recover eukaryotic MAGs using CONCOCT, metaBAT2 and EukCC's merging algorythm. Needs paired end shotgu...
paired sequencing data eukcc Biopython BUSCO dRep MetaWRAP Minimap2 SAMtools Snakemake pysam Sequence analysis
Free
20
rnaseq-pe-main
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RNA-seq paired-end Workflow
public

public

The workflow needs a list of dataset pairs of fastqsanger. As well as a gtf file with genes Optional, but recommen...
FASTQ paired sequencing data Mapping Ontology mapping BEDTools Cufflinks Cutadapt Galaxy MultiQC STAR WorkflowHub RNA-Seq
Free