Tool and database overview
August 26, 2026 ยท View on GitHub
Databases general
| database | used for | last update/check | notes | url |
|---|---|---|---|---|
| dbSNP | pipeline | 04.2026 (b157) | https://ftp.ncbi.nih.gov/snp/archive/ | |
| ClinGen | pipeline | 04.2026 (latest - not versioned) | https://ftp.clinicalgenome.org/ | |
| RepeatMasker | pipeline | 04.2026 (4.0.5) | https://www.repeatmasker.org/species/hg.html | |
| ClinVar (SNVs and CNVs) | pipeline, NGSDImportHPO | 04.2026 (20260329) | update IGV custom tracks in GSvar (with TBI index!) | https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2025/ |
| HGNC | pipeline, NGSDImportHGNC | 04.2026 (2026-04-07) | https://www.genenames.org/download/archive/monthly/tsv/ | |
| gnomAD (genome) | pipeline | 04.2026 (4.1) | https://gnomad.broadinstitute.org/downloads | |
| gnomAD (constraints) | NGSDImportGeneInfo | 04.2026 (4.1.1) | https://gnomad.broadinstitute.org/downloads | |
| phyloP | pipeline | 04.2026 (05.2015) | https://hgdownload.soe.ucsc.edu/goldenPath/hg38/phyloP100way/ | |
| CADD | pipeline | 04.2026 (1.7) | https://cadd.bihealth.org/download | |
| REVEL | pipeline | 04.2026 (1.3) | https://sites.google.com/site/revelgenomics/downloads | |
| AlphaMissense | pipeline | 04.2026 (03.08.2023) | https://console.cloud.google.com/storage/browser/dm_alphamissense | |
| OMIM | pipeline, NGSDImportHPO, NGSDImportOMIM | 03.2026 (latest - not versioned) | https://omim.org/downloads/ | |
| HGMD (SNVs and CNVs) | pipeline | 04.2026 (2026.1) | update IGV custom tracks in GSvar (with TBI index!) | https://apps.ingenuity.com/ingsso/login |
| Ensembl | pipeline, NGSDImportEnsembl | 09.2025 (115) | update IGV genome, update GSvar transcript matches using TranscriptComparison | https://ftp.ensembl.org/pub/release-115/gff3/homo_sapiens/ |
| HPO | NGSDImportHPO | 04.2026 (2026-02-16) | send updated HPO list to Anne (scripts/2021_10_21_hpo_update/) | https://github.com/obophenotype/human-phenotype-ontology |
| GenCC | NGSDImportHPO | 04.2026 (latest - not versioned) | https://search.thegencc.org/download | |
| G2P | NGSDImportHPO | 04.2026 (2026-03-28) | https://ftp.ebi.ac.uk/pub/databases/gene2phenotype/G2P_data_downloads/ | |
| ORPHA | NGSDImportORPHA | 04.2026 (latest - not versioned) | Products 1 and 6 are updated twice a year only (July and December) | https://github.com/Orphanet |
| OncoTree | NGSDImportOncotree | 04.2026 (2025_10_03) | https://github.com/cBioPortal/oncotree/tree/master/trees | |
| CSpec | NGSDImportCSpec | 04.2026 (latest - not versioned) | https://cspec.genome.network/ |
Databases for somatic pipelines
| database | used for | last update/check | notes | url |
|---|---|---|---|---|
| CancerHotspots | pipeline (somatic) | 10.2025 | version is final and does not change - lifted version at data/misc/cancerhotspots | https://www.cancerhotspots.org |
| NCG7.2 | pipeline (somatic) | 10.2025 (v7.2) | manually update data/gene_lists/somatic_tmb_tsg.bed if NCG file changes | http://ncg.kcl.ac.uk/ |
| COSMIC CMC | pipeline (somatic) | 10.2025 (v102) | https://cancer.sanger.ac.uk/cmc | |
| Human Protein Atlas | pipeline (somatic) | 10.2025 (v24) | https://www.proteinatlas.org/about/download |
Databases for RNA pipelines
| database | used for | last update/check | notes | url |
|---|---|---|---|---|
| Ensembl GTF file | pipeline (RNA) | 01.2026 (kept on ensembl v109) | Keep at V109 as the NGSD import is based on these transcripts - if updated also remake STAR index | https://ftp.ensembl.org/pub/release-109/gtf/homo_sapiens/ |
Tools general
| tool | used for | last update/check | notes | url |
|---|---|---|---|---|
| ngs-bits | annotation, quality control, ... | 01.2026 (2025_09) | ||
| samtools | BAM sorting | 01.2026 (1.23) | if updated, update samtools in containers as well: grep samtools data/tools/container_recipes/*.def | https://github.com/samtools/samtools/releases/ |
| bwa2 | mapping (default) | 01.2026 (2.2.1) | https://github.com/bwa-mem2/bwa-mem2 | |
| bwa | mapping (if use_bwa1 is true in settings) | 01.2026 (0.7.19) | https://github.com/lh3/bwa/ | |
| samblaster | duplicate removal | 01.2026 (0.1.26) | https://github.com/GregoryFaust/samblaster | |
| freebayes | variant calling | 01.2026 (1.3.10) | https://github.com/ekg/freebayes | |
| vcflib | VCF normalization | 01.2026 (1.0.3) | version 1.0.14 available, but not updated because we want to remove vcflib asap | https://github.com/vcflib/vcflib |
| ClinCNV | CNV calling | 02.2026 (1.19.1) | https://github.com/imgag/ClinCNV | |
| manta | structural variant calling | 01.2026 (1.6.0) | https://github.com/Illumina/manta | |
| InterOp | reading InterOp metric files (Illumina NextSeq 1k/2k) | 01.2026 (1.2.4) | version 1.9.0 available but update not necessary | https://github.com/Illumina/interop |
| Circos | circos plot with CNVs,ROHS,etc | 01.2026 (0.69.9) | https://circos.ca/software/download/ | |
| ExpansionHunter | Repeat expansion calling | 01.2026 (5.0.0) | https://github.com/Illumina/ExpansionHunter | |
| SpliceAI | Predict splicing variant effect | 01.2026 (1.3.1) | https://github.com/Illumina/SpliceAI | |
| REViewer | Repeat expansion visualization | 01.2026 (0.2.7) | https://github.com/Illumina/REViewer | |
| ORAD | Illumina ORA file decompression | 01.2026 (2.6.1) | version 2.7.0 available but update not necessary | |
| DeepVariant | variant calling | 01.2026 (1.9.0) | https://github.com/google/deepvariant/ | |
| HTSlib | Compressing and indexing files | 01.2026 (1.23) | https://github.com/samtools/htslib |
Tools for somatic pipelines
| tool somatic | used for | last update/check | notes | url |
|---|---|---|---|---|
| strelka2 | variant calling (tumor/normal) | 01.2026 (2.9.10) | https://github.com/Illumina/strelka | |
| msisensor-pro | microsatelite instability (tumor/normal) | 01.2026 (v1.3.0) | https://github.com/xjtu-omics/msisensor-pro | |
| varscan2 | variant calling | 01.2026 (2.4.6) | https://github.com/dkoboldt/varscan | |
| umiVar2 | variant calling cfDNA | 11.2025 (2025_08) | https://github.com/imgag/umiVar2 | |
| hla-genotyper | HLA genotyping | 01.2026 (2025_04) | https://github.com/axelgschwind/hla-genotyper | |
| SigProfilerExtractor | mutational signatures | 01.2026 (1.2.6) | https://github.com/AlexandrovLab/SigProfilerExtractor | |
| DeepSomatic | variant calling (tumor/normal + tumor/only) | 12.2025 (1.9.0) | https://github.com/google/deepsomatic |
Tools for RNA pipeline
| tool RNA | used for | last update/check | notes | url |
|---|---|---|---|---|
| STAR | mapping | 04.2026 (2.7.11b) | https://github.com/alexdobin/STAR | |
| subread | read counting | 04.2026 (2.1.1) | https://subread.sourceforge.net/ | |
| Arriba | fusion detection | 04.2026 (2.5.1) | https://github.com/suhrig/arriba | |
| Kraken2 | fastq filtering | 04.2026 (2.17.1) | https://github.com/DerrickWood/kraken2 | |
| umi_tools | UMI extraction | 04.2026 (1.1.6) | https://github.com/CGATOxford/UMI-tools |
Tools for longread pipeline
| tool longread | used for | last update/check | notes | url |
|---|---|---|---|---|
| minimap2 | mapping | 04.2026 (2.30) | https://github.com/lh3/minimap2 | |
| clair3 | small variant calling | 11.2025 (1.2.0) | currently not in use, we also use DeepVariant for ONT/PacBio data | https://github.com/HKU-BAL/Clair3 |
| clair-mosaic | small variant calling for mosaic variants | 04.2026 (0.1.0) | currently only used for ONT samples | https://github.com/HKU-BAL/Clair-Mosaic |
| Himito | small variant calling for mito variants | 08.2026 (v1.1.2) | used for ONT and PacBio samples | https://github.com/broadinstitute/Himito |
| longphase | phasing | 04.2026 (v2.0.1) | https://github.com/twolinin/longphase | |
| sniffles | structural variant calling | 03.2026 (v2.7.2) | used for ONT samples | https://github.com/fritzsedlazeck/Sniffles |
| sawfish | structural variant calling for PacBio | 08.2026 (v2.2.1) | used for PacBio samples | https://github.com/PacificBiosciences/sawfish |
| straglr | repeat expansion caller | 11.2025 (v1.5.5) | https://github.com/bcgsc/straglr | |
| straglrOn | repeat expansion visualization | 04.2026 (v0.2.4) | https://github.com/leonschuetz/StraglrOn | |
| modkit | methylation extraction | 11.2025 (v0.5.0) | https://github.com/nanoporetech/modkit | |
| methylartist | methylation plots | 04.2026 (v1.5.3) | https://github.com/adamewing/methylartist | |
| paraphase | pseudo-gene calling | 04.2026 (v3.3.1) | last version without PacBio license (can be used only for PacBio data) | https://github.com/PacificBiosciences/paraphase |
| dorado | basecaller for ONT | 04.2026 (v1.4.0) | https://github.com/nanoporetech/dorado |