All Published Workflows
231 workflows that have been reviewed and published
![dna-seq-gatk-variant-calling](https://media.bioworkflows.com/bioworkflows/public_preview/4b8eed0f6a179f18a43e601e653aee298718468aaf37ee1b3d0f8dddaffcaf6a.jpg)
This Snakemake pipeline implements the GATK best-practices workflow
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
![dna-seq-varlociraptor](https://media.bioworkflows.com/bioworkflows/public_preview/d340f005ebb434d0f6a6cb675215dd3df9d4a4e20a9e384a028fcb5cfcf3209d.jpg)
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON
raw sequence reads
Variant calling
genetic variants
delly
gatk
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
BEDTools
Bowtie 2
BWA
Cutadapt
FastQC
fgbio
FreeBayes
mosdepth
MultiQC
Pandas
Picard
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
numpy
oschmod
sklearn
statsmodels
Varlociraptor
DNA
![lathe](https://media.bioworkflows.com/bioworkflows/public_preview/1f180f3eaf10aa1f49825688bd4634606b3e4c92a2d6c655dd34486bf7715039.jpg)
A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing
A tool for generating bacterial genomes from metagenomes with Nanopore long read sequencing First, install miniconda3 The...
![covid-19-signal](https://media.bioworkflows.com/bioworkflows/public_preview/654963db437af051ec1197e3ab2a3eb4c6cbdc09928cdc2b32ea2aa3d58d2787.jpg)
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
![mapache](https://media.bioworkflows.com/bioworkflows/public_preview/bb656e17ac94b23426305db1b39bff6177b185cdd574346d96093c6f5281264c.jpg)
mapping pipeline for ancient DNA
Mapache ([maˈpa.t͡ʃe]) is a lightweight mapping pipeline for ancient DNA using the workflow manager Snakemake . Visit ...
![varca](https://media.bioworkflows.com/bioworkflows/public_preview/ca7f9ec8a74e09f79d5d2c1771189892e2bd70592bd3457dadde86e34364ea4b.jpg)
Use an ensemble of variant callers to call variants from ATAC-seq data
A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
![snparcher](https://media.bioworkflows.com/bioworkflows/public_preview/c9f74c852c98b1e60fc1f38c2e86ef69d22a305ec0adb59be678dcb2f476bf13.jpg)
Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
snpArcher is a reproducible workflow optimized for nonmodel organisms and comparisons across datasets, built on the Snakema...
![uncovar](https://media.bioworkflows.com/bioworkflows/public_preview/81f9768cc8e6e96ca0b24ce2ae4ce244b89d0d4e8b1a84b7a7a33388e8e7b0ae.jpg)
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
A reproducible and scalable workflow for transparent and robust SARS-CoV-2
variant calling and lineage assignment with com...
JSON
raw sequence reads
Variant calling
genetic variants
delly
nanofilt
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
Biopython
BWA
CANU
Consensus
fastp
FastQC
fgbio
FreeBayes
GFFutils
kallisto
Kraken
Krona
Medaka
metaspades
Minimap2
MultiQC
Pandas
Pangolin
Picard
Quant
QUAST
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
altair
intervaltree
numpy
pysam
requests
Varlociraptor
COVID19 Risk Mitigation
![mosaicatcher-pipeline](https://media.bioworkflows.com/bioworkflows/public_preview/c48c164807fd814e269fb9d2bd621165c0b5c3e492cd94db57e6d55999df4ed1.jpg)
Integrated workflow for SV calling from single-cell Strand-seq data
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
![dna-seq-neoantigen-prediction](https://media.bioworkflows.com/bioworkflows/public_preview/567dd1c7d8df937875297f21b13a6921a21676de385d24ca874095af9ddecec1.jpg)
Neoantigen Prediction Snakemake Workflow: Genomic Variant Detection and Peptidome Incorporation
This workflow detects genomic variants with Strelka and and tries to incorporate germline and somatic variants into a sam...
Sequence
Genetic variation analysis
genetic variants
gatk
hla-la
rust-bio-tools
tabix
Arriba
BCFtools
BWA
Cutadapt
FreeBayes
kallisto
Microphaser
NetMHCIIpan
NetMHCpan
Pandas
Picard
Quant
razers3
SAMtools
Snakemake
STAR
Strelka
Variant Effect Predictor (VEP)
vembrane
Jinja2
numpy
Varlociraptor
Genomics
![bo-demography](https://media.bioworkflows.com/bioworkflows/public_preview/ebaad6be60a2cfbd7e3eba5cc147b7d423f34110178ca07c9c11b6bc1ac9135b.jpg)
Demographic analysis of Brassica oleracea
Demographic analysis of Brassica oleracea Follows GATK4 best practices (https://software.broadinstitute.org/gatk/best-practic...
![genome-seek](https://media.bioworkflows.com/bioworkflows/public_preview/74d1cdf281aea78472b3d9566e5a748f5cf5daa7fd4c4cdc2aeb97eed7930678.jpg)
Clinical Whole Genome Sequencing Pipeline
Whole Genome Clinical Sequencing Pipeline.
This is the home of the pipeline, genome-seek. Its long-term goals: to ac...