All Published Workflows

JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode

raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics

raw sequence reads Read pre-processing Report umi_tools BBMap Biopython Cutadapt FastQC MultiQC Seurat Snakemake STAR devtools dplyr ggplot2 gridExtra Matrix plotly plyr RColorBrewer stringr tidyr viridis yaml pysam scRNAseq data processing

JSON Expression data Expression analysis Expression data bioawk snakemake-wrapper-utils biomaRt IHW Biopython BWA CPAT Cutadapt fgsea graphite GSEA IsoformSwitchAnalyzeR kallisto limma Pandas pheatmap Picard Quant SAMtools sleuth Snakemake SPIA dplyr fs ggplot2 ggpubr gridExtra tidyr tidyverse altair altair-saver goatools matplotlib numpy pysam scipy RNA-Seq

scp Biopython Consensus Diamond HHblits hmmsearch (genouest) Kaiju MMseqs Snakemake

JSON raw sequence reads Variant calling genetic variants delly nanofilt rust-bio-tools snakemake-wrapper-utils tabix BCFtools Biopython BWA CANU Consensus fastp FastQC fgbio FreeBayes GFFutils kallisto Kraken Krona Medaka metaspades Minimap2 MultiQC Pandas Pangolin Picard Quant QUAST SAMtools Snakemake Variant Effect Predictor (VEP) vembrane altair intervaltree numpy pysam requests Varlociraptor COVID19 Risk Mitigation

JSON csvtk nextclade Biopython CLICK Pandas Pangolin seqkit Snakemake epiweeks functions matplotlib numpy pango-aliasor PyYAML requests

snpsplit Biopython bsseq BWA DSS GenomicRanges HISAT2 nanopolish SAMtools Snakemake Bismark broom data.table dplyr magrittr readr tidyverse numpy pysam Trim_Galore

JSON CleanEx dataset code Clustering Text mining report bigslice refseq_masher antiSMASH Biopython cblaster CheckM Diamond eggNOG-mapper v2 FastANI metaprokka MLST Pandas Peppy Roary seqfu Snakemake alive-progress gtdbtk matplotlib ncbi-genome-download networkx numpy plotly PyYAML requests Comparative genomics

Barrnap prodigal MEGAHIT Biopython BLAST Bowtie 2 Centrifuge CheckM contigtax Cutadapt edgeR eggNOG-mapper v2 FastANI FastQC FeatureCounts Infernal cmscan (EBI) kraken2 Krona MaxBin MetaBAT 2 metagenomeSeq MetaPhlAn metaspades MultiQC Pandas Picard SAMtools seqtk Snakemake SortMeRNA SqueezeMeta Trimmomatic Trnascan-SE CONCOCT common gtdbtk networkx numpy RGI

bigWig ucsc-liftover BiocParallel Biopython Biostrings BSgenome Consensus GenomicAlignments GenomicFeatures GenomicRanges HiTC Pandas Picard rtracklayer SAMtools Snakemake STAR Trimmomatic corrplot eulerr factoextra GGally ggplot2 ggpubr ggrepel gridExtra here kableExtra Matrix optparse plotly pROC readxl tidyverse numpy plotly

prodigal-gv virsorter Biopython cd-hit Snakemake