All Published Workflows

93 workflows that have been reviewed and published

natrix
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Open-source bioinformatics pipeline for the preprocessing of raw sequencing data.
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public

Natrix is an open-source bioinformatics pipeline for the preprocessing of raw sequencing data. The need for a scalable, repro...
raw sequence reads Primer removal Quality control report dada2 BLAST cd-hit Cutadapt FastQC MultiQC Pandas PANDAseq seqtk ShortRead Snakemake Swarm VSEARCH AmpliconDuo data.table ggplot2 xtable dinopy numpy PyYAML tables Function analysis
Free
44
varca
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Use an ensemble of variant callers to call variants from ATAC-seq data
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public

A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
VCF Data Variant calling genetic variants delly macs2 tabix BCFtools BEDTools BWA Pandas SAMtools Snakemake BBmisc data.table dplyr ggplot2 parallelMap plyr R.devices matplotlib numpy pysam sklearn ATAC-seq deep learning
Free
39
mosaicatcher-pipeline
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Integrated workflow for SV calling from single-cell Strand-seq data
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Structural variant calling from single-cell Strand-seq data Snakemake pipeline. This workflow uses Snakemake to execu...
mosaicatcher tabix BCFtools BEDTools ComplexHeatmap Pandas pheatmap SAMtools Snakemake TensorFlow WhatsHap assertthat BiocManager cowplot data.table devtools dplyr ggnewscale ggplot2 ggpubr matrixStats optparse RColorBrewer reshape reshape2 scales stringr tibble tidyr intervaltree matplotlib numpy parmap plotly pysam PyYAML scipy seaborn tqdm xopen
Free
202
haplotyped-methylome
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Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
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public

Reproducibility instructions for Gigante et al., 2019. Note: this repository is still being tested! If you find a bug, plea...
snpsplit Biopython bsseq BWA DSS GenomicRanges HISAT2 nanopolish SAMtools Snakemake Bismark broom data.table dplyr magrittr readr tidyverse numpy pysam Trim_Galore
Free
116
rna-seq-pop
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Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
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Documentation : https://sanjaynagi.github.io/rna-seq-pop/ Walkthrough : https://www.youtube.com/watch?v=5QQe7DLHO4...
FASTQ-illumina JSON Sample annotation Variant calling genetic variants snakemake-wrapper-utils EnhancedVolcano BCFtools DESeq2 fastp FreeBayes GLUE HISAT2 kallisto mosdepth MultiQC Pandas pheatmap Quant SAMBLASTER SAMtools sleuth Snakemake snpEff Vcflib data.table dplyr ggplot2 ggrepel jsonlite openxlsx RColorBrewer tidyverse ipykernel matplotlib matplotlib-venn numpy papermill pop-tools scipy zarr Population genomics
Free
63
invitrospi
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Spliced peptide identification from in vitro digestions of polypeptides with purified proteasomes
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public

Spliced peptide identification from in vitro digestions of polypeptides with purified proteasomes Please cite the following p...
Snakemake data.table dplyr ggplot2 gridExtra plyr seqinr stringr
Free
8
bollito
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A single-cell RNA-seq pipeline
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public

Pipeline status bollito is a Snakemake pipeline that performs a comprehensive single-cell RNA-seq analysis, co...
GenomeInfoDbData qusage slingshot BiocParallel Bowtie 2 FastQC GFFutils GSEA MultiQC patcHwork pheatmap SCANPY Seurat SingleCellExperiment Snakemake STAR cluster clustree data.table devtools dplyr future ggplot2 htmltools Matrix openxlsx RColorBrewer reticulate rgl rmarkdown scales stringr viridis SeuratDisk SeuratWrappers
Free
50
cnvbench
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Benchmarking of CNV calling tools
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This pipeline was set up to test a variety of CNV calling tools on WES and WGS samples sequenced using Illumina short-read se...
gatk BEDTools BWA mosdepth rtracklayer SAMtools Snakemake data.table lubridate yaml
Free
13
alphscore
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Improving pathogenicity prediction of missense variants by using AlphaFold-derived features
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public

This code belongs to the project "Predicting the pathogenicity of missense variants using features derived from AlphaFold2". ...
tabix Biopython Pandas Snakemake boot caret data.table dplyr ggplot2 gridExtra optparse pROC PRROC ranger readr readxl stringr tidyverse VennDiagram biographs biopandas networkx numpy pdbparser
Free
50
cardiopipeline
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Pipeline for RNA-seq analysis
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This is a simple utility to analyse RNA-seq data with a selection of popular tools. It is written in snakemake that allow...
DESeq2 SortMeRNA tximport AnnotationDbi BEDTools Bowtie 2 DESeq2 kallisto MashMap MultiQC Rsubread Salmon Snakemake SRA data.table
Free
28
arpeggio
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A SnakeMake workflow to analyse whole genome bisulfite sequencing data from allopolyploids.
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ARPEGGIO is a snakemake workflow that analyzes whole genome bisulfite sequencing (WGBS) data coming from (allo)polyploid spec...
BEDTools BiocParallel Cutadapt dmrseq FastQC MultiQC QualiMap SAMtools Snakemake Bismark data.table stringr Trim_Galore
Free
73
ukb-gwas-pipeline-nealelab
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Pipeline for reproduction of NealeLab 2018 UKB GWAS
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This pipeline is a WIP, but it will attempt to reproduce this GWAS (with associated code at UK_Biobank_GWAS ) using ...
FIRE Pandas Snakemake data.table dask fsspec gcsfs numpy retrying sgkit xarray zarr
Free
28