Similar to audy’s stitch program, but in C, more efficient and supports some automatic benchmarking and tuning. It uses the same “squared distance for anchored alignment” as other tools.
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install fastq-join
and update with:
conda update fastq-join
A Docker container is available at https://quay.io/repository/biocontainers/fastq-join.