# Kraken Benchmark

## Input files

This benchmark runs on the HiSeq and MiSeq data from Kraken. These are found in `HiSeq_accuracy.fa` and `MiSeq_accuracy.fa`. Using their README (`ACCURACY.README`), we wrote `header2id.sed` to replace the complex fasta headers with just taxon ids and a unique number. This will simplify measuring the results later.

## Benchmark

The `benchmark` script contains the several pipelines. I'm still thinking on how to run these on e.g. the HPC. For now, it just contains one pipeline.