diff --git a/README.md b/README.md index 500ca16..380e62b 100644 --- a/README.md +++ b/README.md @@ -21,6 +21,12 @@ **nf-core/variantbenchmarking** is designed to evaluate and validate the accuracy of variant calling methods in genomic research especially for Human data. Initially, the pipeline is tuned well for available gold standard truth sets (for example, Genome in a Bottle and SEQC2 samples) but it can be used to compare any two variant calling results. The workflow provides benchmarking tools for small variants including SNVs and INDELs, Structural Variants (SVs) and Copy Number Variations (CNVs) for germline and somatic analysis. +The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! + +

+ +

+ The workflow involves several key processes to ensure reliable and reproducible results as follows: ### Standardization and normalization of variants: @@ -149,8 +155,14 @@ nf-core/variantbenchmarking was originally written by Kübra Narcı ([@kubranarc We thank the following people for their extensive assistance in the development of this pipeline: -Nicolas Vannieuwkerke ([@nvnienwk](https://github.com/nvnieuwk)) -Maxime Garcia ([@maxulysse](https://github.com/maxulysse)) +- Nicolas Vannieuwkerke ([@nvnienwk](https://github.com/nvnieuwk)), +- Maxime Garcia ([@maxulysse](https://github.com/maxulysse)) + +## Acknowledgements + + + GHGA + ## Contributions and Support diff --git a/docs/images/GHGA_short_Logo_orange.png b/docs/images/GHGA_short_Logo_orange.png new file mode 100644 index 0000000..180996f Binary files /dev/null and b/docs/images/GHGA_short_Logo_orange.png differ diff --git a/docs/images/mqc_fastqc_adapter.png b/docs/images/mqc_fastqc_adapter.png deleted file mode 100755 index 361d0e4..0000000 Binary files a/docs/images/mqc_fastqc_adapter.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_counts.png b/docs/images/mqc_fastqc_counts.png deleted file mode 100755 index cb39ebb..0000000 Binary files a/docs/images/mqc_fastqc_counts.png and /dev/null differ diff --git a/docs/images/mqc_fastqc_quality.png b/docs/images/mqc_fastqc_quality.png deleted file mode 100755 index a4b89bf..0000000 Binary files a/docs/images/mqc_fastqc_quality.png and /dev/null differ diff --git a/docs/images/variantbenchmarking_metromap.png b/docs/images/variantbenchmarking_metromap.png new file mode 100644 index 0000000..4cccd62 Binary files /dev/null and b/docs/images/variantbenchmarking_metromap.png differ diff --git a/docs/images/variantbenchmarking_metromap.svg b/docs/images/variantbenchmarking_metromap.svg new file mode 100644 index 0000000..53c1c70 --- /dev/null +++ b/docs/images/variantbenchmarking_metromap.svg @@ -0,0 +1,3507 @@ + + + + + + + + + + + + + + + + + + benchmarkingSingle-sampleMultiple-sampleTest preprocessingOutput preprocessingStructural variants onlyAll variantsLegendOptional processesSmall variants onlySomatic variants onlyTruth preprocessingbcftools viewpicard CreateSequenceDictionaryUCSCliftoverpicard LiftoverVcfvariant extractorsvyncbcftools mergeSURVIVORmergeVCF to CSVmerge summarystatsdatavzrdplotsummarystatssompyhappyrtgtoolstruvariwittyersvbenchmarkfilter contigsbcftools filterSURVIVORfilterbcftools statsSURVIVORstatsbcftools reheaderTEST (QUERY) VCFs bcftools normprepysplitSNVsINDELsbcftools dedupfiltrationsvariant statistics--preprocessing--sv_standardization--liftoversumary reportingTRUTH (BASE) VCFs + High Confidence BEDs genomev1.0.0chaingenomebedvcfvcfvcffastafastachainrename chromosomestxtsdfstatsstatsrochtmlpngcsvvcf