bioxflow/wgs
In developmentWhole-genome sequencing
Read quality control, trimming, alignment and variant calling for whole-genome sequencing data.
wgsalignmentvariants
FastQC · fastp · BWA-MEM2 · SAMtoolsNextflow
Catalogue
Pipelines
Reproducible analysis pipelines developed and reviewed by the Bioxflow community.
bioxflow/rnaseq
ReleasedBulk RNA-seq
FASTQ to differential expression. Every sample is quantified twice, by Salmon and by STAR, and the two results are compared before DESeq2 runs.
rna-seqgene-expressiondeseq2concordance
fastp · Salmon · STAR · DESeq2 · MultiQCNextflow
bioxflow/scrnaseq
PlannedSingle-cell RNA-seq
QC, normalisation, dimensionality reduction, clustering and cell-type annotation of single-cell data.
scrna-seqclusteringannotation
Scanpy · Seurat · scvi-toolsNextflow
bioxflow/amr
In developmentAntimicrobial resistance genomics
Assembly and annotation of bacterial genomes with detection of resistance genes, virulence factors and mobile elements.
amrbacteriaannotation
AMRFinderPlus · ABRicate · Prokka · BLASTNextflow
bioxflow/variantcall
PlannedGermline variant analysis
Alignment, variant calling, filtering and functional annotation of germline variants.
vcfgatkannotation
BWA · GATK · BCFtools · VEPNextflow
bioxflow/metagenomics
PlannedShotgun metagenomics
Read QC, taxonomic profiling and microbial community analysis for shotgun metagenomic samples.
microbiometaxonomyprofiling
Kraken2 · Bracken · MetaPhlAn · MultiQCSnakemake
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