Auto-generated from
%labelsin recipe files. Runpython utilities/generate_catalogue.pyto refresh.
| Tool | Version | Description | Pull |
|---|---|---|---|
| facets | latest | Allele-specific copy number analysis from tumour/normal sequencing | apptainer pull oras://ghcr.io/brucemoran/singularity/facets--latest:latest |
| qdnaseq | latest | Quantitative DNA sequencing copy number analysis | apptainer pull oras://ghcr.io/brucemoran/singularity/qdnaseq--latest:latest |
| sequenza | latest | Cancer cellularity and ploidy estimation from sequencing | apptainer pull oras://ghcr.io/brucemoran/singularity/sequenza--latest:latest |
| SomaticSignatures | see recipe | Somatic mutation signature extraction and analysis | apptainer pull oras://ghcr.io/brucemoran/singularity/somaticsignatures--latest:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| bwa | 0.7.17 | Burrows-Wheeler Aligner for short-read DNA alignment | apptainer pull oras://ghcr.io/brucemoran/singularity/bwa--0-7-17:latest |
| kallisto | 0.45.0 | RNA-seq pseudoalignment-based transcript quantification | apptainer pull oras://ghcr.io/brucemoran/singularity/kallisto--0-45-0:latest |
| minimap2 | git-7bc87b4 | Long-read and short-read sequence aligner | apptainer pull oras://ghcr.io/brucemoran/singularity/minimap2--latest:latest |
| star | 2.7.0b | Spliced Transcripts Alignment to a Reference (RNA-seq aligner) | apptainer pull oras://ghcr.io/brucemoran/singularity/star--2-7-0b:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| pcgr | latest | Personal Cancer Genome Reporter for variant annotation | apptainer pull oras://ghcr.io/brucemoran/singularity/pcgr--centos7:latest |
| pcgr | latest | Personal Cancer Genome Reporter for variant annotation | apptainer pull oras://ghcr.io/brucemoran/singularity/pcgr--docker:latest |
| VEP 92.1 | 92.1 | Ensembl Variant Effect Predictor | apptainer pull oras://ghcr.io/brucemoran/singularity/vep--92-1:latest |
| VEP 92.1.homo sapiens merged.GRCh37 | 92.1 | Ensembl Variant Effect Predictor | apptainer pull oras://ghcr.io/brucemoran/singularity/vep--92-1--homo--sapiens--grch37:latest |
| VEP 92.1.homo sapiens merged.hg38 | 92.1 | Ensembl Variant Effect Predictor | apptainer pull oras://ghcr.io/brucemoran/singularity/vep--92-1--homo--sapiens--hg38:latest |
| VEP 92.1.rattus norvegicus merged | 92.1 | Ensembl Variant Effect Predictor | apptainer pull oras://ghcr.io/brucemoran/singularity/vep--92-1--rattus--norvegicus:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| rockylinux9-base | 9.4 | Rocky Linux 9 base image for modern HPC container builds | apptainer pull oras://ghcr.io/brucemoran/singularity/rockylinux9--9-4:latest |
| rockylinux9-conda | 9.4 | Rocky Linux 9 base image with Miniforge for reproducible Conda environments | apptainer pull oras://ghcr.io/brucemoran/singularity/rockylinux9--conda--9-4:latest |
| rockylinux9-java17 | 9.4 | Rocky Linux 9 base image with OpenJDK 17 for modern genomics tools | apptainer pull oras://ghcr.io/brucemoran/singularity/rockylinux9--java17--9-4:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| cnvnator | latest | Copy number variant detection from read-depth analysis | apptainer pull oras://ghcr.io/brucemoran/singularity/cnvnator--latest:latest |
| guppy | latest | Oxford Nanopore basecaller | apptainer pull oras://ghcr.io/brucemoran/singularity/guppy--latest:latest |
| nanostat | latest | Statistical summary of Oxford Nanopore sequencing reads | apptainer pull oras://ghcr.io/brucemoran/singularity/nanostat--latest:latest |
| pbsv | latest | PacBio structural variant caller | apptainer pull oras://ghcr.io/brucemoran/singularity/pbsv--latest:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| aracne ap viper | latest | ARACNe-AP regulatory network analysis with VIPER | apptainer pull oras://ghcr.io/brucemoran/singularity/aracne-viper--latest:latest |
| RNAseq kallisto | 0.45.0 | RNA-seq pseudoalignment-based transcript quantification | apptainer pull oras://ghcr.io/brucemoran/singularity/rnaseq-kallisto--latest:latest |
| somatic n of 1 | see recipe | n-of-1 somatic cancer mutation analysis pipeline | apptainer pull oras://ghcr.io/brucemoran/singularity/somatic-n-of-1--latest:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| bbduk | 38.36 | BBDuk read trimmer and quality filter from BBTools | apptainer pull oras://ghcr.io/brucemoran/singularity/bbduk--38-36:latest |
| bcftools | 1.9 | VCF/BCF file manipulation and variant calling toolkit | apptainer pull oras://ghcr.io/brucemoran/singularity/bcftools--1-9:latest |
| bedtools | 2.27.1 | Genome arithmetic toolkit for interval operations | apptainer pull oras://ghcr.io/brucemoran/singularity/bedtools--2-27-1:latest |
| fastp | git-e01e940 | Fast all-in-one FASTQ preprocessor | apptainer pull oras://ghcr.io/brucemoran/singularity/fastp--latest:latest |
| fastqc | 0.11.8 | Quality control analysis tool for sequencing data | apptainer pull oras://ghcr.io/brucemoran/singularity/fastqc--0-11-8:latest |
| gatk4 | 4.1.0 | Genome Analysis Toolkit v4 (Broad Institute) | apptainer pull oras://ghcr.io/brucemoran/singularity/gatk4--4-1-0:latest |
| liftover | latest | UCSC genome coordinate conversion tool | apptainer pull oras://ghcr.io/brucemoran/singularity/liftover--latest:latest |
| multiqc | 1.7 | Aggregate bioinformatics analysis reports across samples | apptainer pull oras://ghcr.io/brucemoran/singularity/multiqc--1-7:latest |
| picard tools | 2.18.26 | Java toolkit for manipulating HTS data (Broad Institute) | apptainer pull oras://ghcr.io/brucemoran/singularity/picard--2-18-26:latest |
| samtools | 1.9 | SAM/BAM/CRAM file manipulation toolkit | apptainer pull oras://ghcr.io/brucemoran/singularity/samtools--1-9:latest |
| Tool | Version | Description | Pull |
|---|---|---|---|
| gridss purple linx.1.2.0 | 1.2.0 | Structural variant, purity and ploidy analysis pipeline | apptainer pull oras://ghcr.io/brucemoran/singularity/gridss-purple-linx--1-2-0:latest |
| lancet | 1.0.7 | Somatic variant caller using micro-assembly | apptainer pull oras://ghcr.io/brucemoran/singularity/lancet--1-0-7:latest |
| manta strelka2 | Manta-1.5.1_Strelka2-2.9.10 | Illumina structural and small somatic variant callers | apptainer pull oras://ghcr.io/brucemoran/singularity/manta-strelka2--1-5-1-2-9-10:latest |
| msisensor | latest | Microsatellite instability analysis from tumour/normal BAMs | apptainer pull oras://ghcr.io/brucemoran/singularity/msisensor--latest:latest |
| octopus | develop | Bayesian haplotype-based variant caller | apptainer pull oras://ghcr.io/brucemoran/singularity/octopus--develop:latest |
| pisces | latest | Illumina variant caller for amplicon or hybrid capture data | apptainer pull oras://ghcr.io/brucemoran/singularity/pisces--latest:latest |
| purecn | latest | Copy number profiling and tumour purity estimation for WES | apptainer pull oras://ghcr.io/brucemoran/singularity/purecn--latest:latest |
| varlociraptor | 1.2.1 | Statistical variant calling with uncertainty quantification | apptainer pull oras://ghcr.io/brucemoran/singularity/varlociraptor--1-2-1:latest |