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. 2021 May 1;22:224. doi: 10.1186/s12859-021-04142-3

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© The Author(s) 2021, corrected publication 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — An example samples.manifest. The samples.manifest file for paired-end samples is composed of five tab separated columns: (1) path to the first FASTQ file in the pair, (2) optional md5 signature for the first FASTQ file in the pair, (3) path to the second FASTQ file in the pair, (4) optional md5 signature for the second FASTQ file in the pair, (5) sample ID. The first two entries use the same sample ID, which is useful when a biological sample was sequenced in multiple lanes and thus generated multiple FASTQ files. The first two pairs of FASTQ files will be merged