Software versions
The main software used by this version of oncoanalyser is listed below. Version changes between releases are recorded
in the CHANGELOG, and the exact versions used in
each run are written to pipeline_info/nf_core_oncoanalyser_software_mqc_versions.yml in the output directory.
WiGiTS tools
Tools from WiGiTS, the open-source suite of genomic analysis tools developed
by the Hartwig Medical Foundation. These tools carry out most of the analysis in oncoanalyser.
| Tool | Version | Description |
|---|---|---|
AMBER |
4.3 | B-allele frequency analysis for purity and ploidy |
BamTools |
1.6.1 | Alignment and coverage metrics |
CHORD |
2.1.2 | Homologous recombination deficiency (HRD) prediction |
CIDER |
1.2 | Immune receptor (IG/TCR) CDR3 sequence detection |
COBALT |
3.0 | GC-normalised read depth ratios |
CUPPA |
2.5.1 | Tissue of origin prediction |
ESVEE |
2.0.1 | Structural variant calling |
FastqTools |
1.0 | UMI extraction from FASTQ read names |
ISOFOX |
2.0.1 | RNA transcript expression and fusion analysis |
LILAC |
2.0 | HLA class I typing and allele-specific status |
LINX |
2.3.1 | SV clustering, fusions and driver event interpretation |
NEO |
1.3 | Neoepitope prediction |
ORANGE |
5.0.1 | Summary report |
PAVE |
1.9 | Gene impact annotation of small variants |
PEACH |
2.0.0 | Pharmacogenomic haplotype calling |
PURPLE |
4.4 | Purity, ploidy and copy number estimation |
QSEE |
1.0 | Sequencing and variant calling QC metrics |
REDUX |
2.0.5 | Duplicate marking, UMI consensus and read unmapping |
SAGE |
5.0.2 | SNV, MNV and INDEL calling |
SIGS |
1.2.1 | Mutational signature fitting |
TEAL |
1.4 | Telomere length and rearrangement characterisation |
VirusInterpreter |
1.7.2 | Oncoviral integration interpretation |
WISP |
1.3.1 | Tumor fraction estimation (purity_estimate mode) |
Other tools
External tools used for read alignment, read processing, oncoviral detection and reporting.
| Tool | Version | Description |
|---|---|---|
BWA-MEM2 |
2.3 | DNA read alignment |
fastp |
0.23.4 | FASTQ splitting and UMI extraction |
GATK4 (Picard MarkDuplicates) |
4.6.1.0 | RNA duplicate marking |
GRIDSS (VIRUSbreakend) |
2.13.2 | Oncoviral detection |
linxreport |
1.2.0 | Interactive LINX report |
MultiQC |
1.35 | Aggregated QC report |
RepeatMasker |
4.1.5 | Repeat annotation for VIRUSbreakend |
sambamba |
1.0.1 | Conversion and sorting of DNA alignments |
samtools |
1.21 | BAM sorting and indexing |
STAR |
2.7.3a | RNA read alignment |