All Published Workflows

FASTQ Sample ID Mapping Taxonomy ngs_te_mapper2 trim-galore RelocaTE2 Snakemake TEMP TEMP2 Whole genome sequencing

Data Imputation Genome report tabix BCFtools SAMtools Snakemake Whole genome sequencing

Data index Whole genome methylation analysis Report kneaddata Bowtie 2 HUMAnN2 MetaPhlAn Snakemake Whole genome sequencing

Genome index Phylogenetic analysis Phylogenetic tree augustus clustalo raxml-ng Biopython BUSCO IQ-TREE MAFFT API (EBI) Pandas Snakemake trimAl Whole genome sequencing

VCF Genome index Regression analysis Quality control report gatk plink2 regenie tabix BCFtools pLink Variant Effect Predictor (VEP) Whole genome sequencing

Variant calling gatk rust-bio-tools BCFtools FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic common matplotlib numpy seaborn Genomics Whole genome sequencing

BWA FastQC Picard QDNAseq SAMtools Singularity Hub Snakemake argparse cowplot dplyr readr rmarkdown stringr tidyr tidyverse Whole genome sequencing

gatk tabix BCFtools MultiQC Picard Snakemake Sequence analysis Whole genome sequencing

gatk BWA Cutadapt gatk_realigner_target_creator Picard SAMtools Snakemake Whole genome sequencing

Variant calling gatk Bwa-mem2 Picard Snakemake Whole genome sequencing

gatk BWA Cutadapt gatk_realigner_target_creator Picard SAMtools Snakemake Whole genome sequencing

gatk tabix SAMtools Snakemake Whole genome sequencing