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mito-scrna
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Mitochondria Variant Discovery Using Snakemake
public

public

https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels- cop...
gatk manta tabix BCFtools Snakemake Trimmomatic Sequence analysis
Free
10
rnastar_dseq2_old_rnaseq
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Snakemake workflow: rna-seq-star-deseq2
public

public

This workflow performs a differential expression analysis with STAR and Deseq2. Johannes Köster (@johanneskoester), https...
BiocParallel Cutadapt DESeq2 Pandas SAMtools Snakemake STAR dplyr yaml numpy pysam scipy
Free
20
refpanel
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Pipeline to build a large human reference panel, using publicly available genomes
public

public

A fully automated and reproducible pipeline for building large reference panels of jointly-called and phased human genomes, a...
gatk shapeit4 tabix BCFtools BEDTools BWA fastp Picard SAMtools Snakemake Variant Effect Predictor (VEP) WhatsHap
Free
72
utr-variants
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Identification of 3' UTR Variants Disrupting Transcript Function Pipeline
public

public

Identify variants occurring in 3’ UTRs that could disrupt the function of a transcript. This project involves: retrieving...
BEDTools genomepy Pandas Pybedtools Snakemake data.table ggplot2 hail numpy pysam utr-variants Function analysis
Free
21
domain-clustering-pipeline
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Pipeline to extract protein domain clusters from sequence data
public

public

This pipeline is designed to automate the prediction of protein domains given only the protein's sequence, based on the metho...
HHblits Snakemake dplyr ggplot2
Free
10
ena-sars-cov-2-nanopore-amplicon-sequencing-analys
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ENA SARS-CoV-2 Nanopore Amplicon Sequencing Analysis Workflow
public

public

Pipeline for mapping SARS-CoV2 nanopore reads using nextflow
FASTQ raw sequence reads Analysis Quality control report tabix Cutadapt Minimap2 SAMtools Whole genome sequencing
Free
7

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