All Published Workflows

Sequence alignment CRAM FASTQ VCF Singularity Hub singularity

FASTQ Sample ID Alignment Count matrix Minimap2 Quant Salmon SAMtools Snakemake stageR dplyr ggplot2 tidyr Gene expression

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

FASTQ raw sequence reads Sequencing quality control Haplotype map gatk BWA FastQC MultiQC Snakemake Trim_Galore Genomics

FASTQ raw sequence reads Filtering Count matrix DeepTools FeatureCounts htseqcount SAMtools Snakemake STAR RNA-Seq

FASTQ raw sequence reads Clustering Histogram isonclust isonclust2 pychopper Snakemake De Novo

Sequence similarity FASTQ Homology-based gene prediction Plot dlcpar hmmer hmmer2 BLAST BLAST (EBI) BTOD HMMER3 HMMER hmmscan (EBI) HMMER phmmer (EBI) OrthoFinder SMI-BLAST Snakemake Comparative genomics

FASTQ Sample annotation Transcriptome assembly Quality control report BBMap BEDTools cd-hit Quant QUAST Salmon Snakemake TransDecoder metagenomics

FASTQ VCF raw sequence reads Variant calling genetic variants snakemake-wrapper-utils tabix BEDTools MLM Pandas Picard SAMtools Snakemake GLnexus matplotlib numpy seaborn Gene regulation

FASTQ Data Quantification Quality control report PCAtools tximport apeglm Cutadapt DESeq2 FastQC MultiQC pheatmap Quant regionReport Salmon sleuth Snakemake vsn ggplot2 readr stringr RNA-Seq

FASTQ Sample annotation Variant calling genetic variants gatk Bowtie 2 FreeBayes Picard SAMtools Snakemake Trimmomatic Metagenomic sequencing

FASTQ raw sequence reads Expression analysis Quality control report FastQC MultiQC Quant Salmon Snakemake Trimmomatic RNA-Seq