Workflows
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A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.
On the respective GitHub folder are available:
- The CWL wrappers and subworkflows for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
Briefly, the workflow performs the following steps:
- Quality control of Illumina reads ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.
On the respective GitHub folder are available:
- The CWL wrappers and subworkflows for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
Briefly, the workflow performs the following steps:
- Quality control of Illumina reads ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:
- Peak calling
- Consensus peak count table generation
- Detection of super-enhancer regions
- Differential binding analysis
On the respective GitHub folder are available:
- The CWL wrappers for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
- Tables of metadata (
EZH2_metadata_CLL.csv
andH3K27me3_metadata_CLL.csv
), based on the same validation ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.
On the respective GitHub folder are available:
- The CWL wrappers for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
- A table of metadata (
mrna_cll_subsets_phenotypes.csv
), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis