A Community for BioMedical Data Analysis Workflows

A collection of workflows and related code snippets.

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filtering
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Variant Filtering Module for VCF Files with Region and Annotation Filters
public

public

Collection of variant filters The module consists of rules used to filter VCF files. Currently the VCFs can be filtered based...
Variant filtering snakemake-wrapper-utils BCFtools Snakemake Variant Effect Predictor (VEP) hydra-genetics pysam PyYAML Genetic variation
Free
6
mdr_mtb-master
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Pipeline for Predicting Antibiotic Resistance in Mycobacterium tuberculosis Using Snakemake
public

public

This snakemake-based pipeline is a tool for predicting antibiotic resistance in Mycobacterium tuberculosis. The tuberculosis ...
biopet-vcffilter snakemake-wrapper-utils BWA Cutadapt FastQC FreeBayes MultiQC Pandas Picard SAMtools Snakemake altair numpy PyVCF Infectious disease
Free
48
snakemap
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Read-mapping against the contig catalogue from metagenomics by illumina and nanopore
public

public

A Snakemake workflow for snakemap A snakemake workflow for read-mapping against the contig catalogue from metagenomics by...
snakemake-wrapper-utils Bowtie 2 Minimap2 SAMtools Snakemake
Free
15
wgs_genotyping
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Revised WGS Genotyping V2 Workflow
public

public

Cristian Gonzalez-Colin (cgonzalez@lji.org) Vijayanand Lab (https://www.lji.org/labs/vijayanand/) La Jolla Institu...
gatk tabix SAMtools Snakemake Whole genome sequencing
Free
33
acastellanii_genome_analysis
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Comparative analysis of the genomes from two Acanthamoeba castellanii strains
public

public

This repository contains scripts and documentation related to the analysis and comparison of the Acanthamoeba castellanii ...
assembly-stats cooler BEDTools Biopython BLAST BUSCO cd-hit Diamond genomepy MaxBin Minimap2 NG-Circos OrthoFinder Pandas patcHwork QUAST seqkit Snakemake topGO dplyr ggplot2 gridExtra readr stringr tibble tidyr tidyverse viridis cooler matplotlib matplotlib-venn numpy reportlab seaborn
Free
57
wur_mapping-variant-calling
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Short read mapping and variant calling
public

public

Link to the repository Step by step guide on how to use my pipelines Click here for an introduction to Snakemake T...
biopet-vcffilter tabix BCFtools Bwa-mem2 FreeBayes QualiMap SAMBLASTER SAMtools Snakemake
Free
9

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