nf-core/eager is a bioinformatics best-practice analysis pipeline for ancient DNA data analysis.
The pipeline uses Nextflow, a bioinformatics workflow tool. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results. It comes with docker / singularity containers making installation trivial and results highly reproducible.
- Create reference genome indices (optional)
- BWA
- Samtools Index
- Sequence Dictionary
- QC with FastQC
- AdapterRemoval for read clipping and merging
- Read mapping with BWA, BWA Mem or CircularMapper
- Samtools sort, index, stats & conversion to BAM
- DeDup or MarkDuplicates read deduplication
- QualiMap BAM QC Checking
- Preseq Library Complexity Estimation
- DamageProfiler damage profiling
- BAM Clipping for UDG+/UDGhalf protocols
- PMDTools damage filtering / assessment
The nf-core/eager pipeline comes with documentation about the pipeline, found in the docs/ directory:
- Installation
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
- Troubleshooting
This pipeline was written by Alexander Peltzer (apeltzer), with major contributions from Stephen Clayton, ideas and documentation from James Fellows-Yates, Raphael Eisenhofer and Judith Neukamm. If you want to contribute, please open an issue and ask to be added to the project - happy to do so and everyone is welcome to contribute here!