All Published Workflows

Sample annotation Primer removal Quality control report bcl2fastq-nextseq consensusfixer demultiplexer indelfixer Augur BWA Consensus iVar lofreq Pandas SAMtools Snakemake Vicuna numpy PyVCF scikit-bio scipy Genomics

Sample annotation Base-calling Alignment sniffles svim bedGraphToBigWig BEDTools Flye GUPPY Minimap2 nanopolish NGMLR Pandas Racon SAMtools Singularity Hub Snakemake wtdbg2 graphmap2 matplotlib numpy oschmod seaborn nanopore

Sample annotation Chromatographic alignment Heat map cooler BEDTools BWA Minimap2 SAMtools Snakemake Genomics

Sample annotation Sequencing quality control Report Augur BEDTools Pangolin SAMtools Snakemake Genomics

Sample annotation Variant calling genetic variants BCFtools SAMtools Snakemake Structural variation

bigWig Sample annotation cis-regulatory element prediction Plot cooltools Snakemake Data architecture, analysis and design

Sample annotation Sequencing quality control Quality control report BEDTools Minimap2 Pandas SAMtools Snakemake caret e1071 stringdist numpy scipy nanopore

Sample annotation Splicing analysis Snakemake STAR Compound libraries and screening RNA-Seq

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

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

Sample annotation Trajectory visualization Alignment DeepTools SAMtools Snakemake RNA-Seq

Sample annotation Mapping Map Bowtie 2 SAMtools Snakemake ggplot2 magrittr reshape2 Data identity and mapping