Welcome to PALEOMIX's documentation!

The PALEOMIX pipeline is a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data, starting from de-multiplexed reads from one or more samples, through sequence processing and alignment, followed by genotyping and phylogenetic inference on the samples. In addition, PALEOMIX aids in metagenomic analysis of the extracts. The pipeline has been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can be of used for both modern and ancient samples to ensure consistent data processing.

If you make use of any part of the PALEOMIX pipeline and/or assosiated tools, then we ask that you kindly cite [Schubert2014].

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Indices and tables