All Published Workflows
212 workflows that have been reviewed and published
Near-real time tracking of SARS-CoV-2 in Connecticut
Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data
ARMOR ( A utomated R eproducible MO dular R NA-seq) is a Snakemake workflow , aimed at performing a ty...
: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
Note An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic inte...
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
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth . The usage of thi...
JSON
Expression data
Expression analysis
Expression data
bioawk
snakemake-wrapper-utils
biomaRt
IHW
Biopython
BWA
CPAT
Cutadapt
fgsea
graphite
GSEA
IsoformSwitchAnalyzeR
kallisto
limma
Pandas
pheatmap
Picard
Quant
SAMtools
sleuth
Snakemake
SPIA
dplyr
fs
ggplot2
ggpubr
gridExtra
tidyr
tidyverse
altair
altair-saver
goatools
matplotlib
numpy
pysam
scipy
RNA-Seq
A Snakemake workflow to run and benchmark structure learning (a.k.a. causal discovery) algorithms for probabilistic graphical models.
Benchpress [1] is a Snakemake workflow where structure learning algorithms, implemented in possibly different lang...
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
StaG Metagenomic Workflow Collaboration
The StaG Metagenomic Workflow Collaboration (mwc) project focuses on providing
a metagenomics analysis workflow suitable for ...
Reproducible workflow for SARS-CoV-2 recombinant sequence detection.
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Note : ncov-recombinant will be deprecated soon as SARS-CoV-2 recombination has evolved beyond the scope of this pip...
Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
Code related to the manuscript
Inferring signaling pathways with probabilistic programming
(Merrell & Gitter, 2020) B...
Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
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
Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)
BGCFlow is a systematic workflow for the analysis of biosynthetic gene clusters across large collections of genomes (p...
JSON
CleanEx dataset code
Clustering
Text mining report
bigslice
refseq_masher
antiSMASH
Biopython
cblaster
CheckM
Diamond
eggNOG-mapper v2
FastANI
metaprokka
MLST
Pandas
Peppy
Roary
seqfu
Snakemake
alive-progress
gtdbtk
matplotlib
ncbi-genome-download
networkx
numpy
plotly
PyYAML
requests
Comparative genomics