All Published Workflows

Genome index Annotation Map BEDTools BLAST fastp FastQC GFF3 Rebase gffread HISAT2 Minimap2 RepeatMasker RepeatModeler SAMtools Snakemake StringTie RNA-Seq

JSON CleanEx dataset code Annotation phenotype report Augur Biopython Consensus FORECasT IQ-TREE Pandas Snakemake matplotlib numpy scipy seaborn statsmodels TreeTime Population genomics

FASTQ raw sequence reads Annotation Ontology mapping Diamond Snakemake taxonomic and functional annotation

Annotation snakemake-wrapper-utils DESeq HTSeq htseqcount SAMtools Snakemake oschmod Sequence analysis

Alignment Annotation Variant calling Variant filtering bamclipper tabix ASPICov BamTools BCFtools BEDTools BWA fastp FastQC FreeBayes IGVtools MultiQC Nextflow PRINSEQ QUAST SAMtools Singularity Hub snpEff SnpSift Trimmomatic WorkflowHub Genomics

FASTA FASTQ VCF Alignment Annotation Filtering Variant calling gatk tabix BCFtools Bwa-mem2 Consensus fastp illumina iVar lofreq Nextflow Pangolin Sambamba SAMtools snpEff Genomics