A fully reproducible and state-of-the-art ancient DNA analysis pipeline
Define where the pipeline should find input data, and additional metadata.
Additional options regarding input data.
Specify locations of references and optionally, additional pre-made indices
Specify where to put output files and optional saving of intermediate files
Less common options for the pipeline, typically set in a config file.
Set the top limit for requested resources for any single job.
Parameters used to describe centralised config profiles. These generally should not be edited.
Skip any of the mentioned steps.
Processing of Illumina two-colour chemistry data.
Options for adapter clipping and paired-end merging.
Options for reference-genome mapping
Options for production of host-read removed FASTQ files for privacy reasons.
Options for quality filtering and how to deal with off-target unmapped reads.
Options for removal of PCR amplicon duplicates that can artificially inflate coverage.
Options for calculating library complexity (i.e. how many unique reads are present).
Options for calculating and filtering for characteristic ancient DNA damage patterns.
Options for getting reference annotation statistics (e.g. gene coverages)
Options for trimming of aligned reads (e.g. to remove damage prior genotyping).
Options for variant calling.
Options for creation of a per-sample FASTA sequence useful for downstream analysis (e.g. multi sequence alignment)
Options for creation of a SNP table useful for downstream analysis (e.g. estimation of cross-mapping of different species and multi-sequence alignment)
Options for the calculation of ratio of reads to one chromosome/FASTA entry against all others.
Options for the calculation of biological sex of human individuals.
Options for the estimation of contamination of human DNA.
Options for metagenomic screening of off-target reads.
Options for authentication of metagenomic screening performed by MALT.