Determining the quality and complexity of next-generation sequencing data without a reference genome |
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| Authors: | Seyed Yahya Anvar Lusine Khachatryan Martijn Vermaat Michiel van Galen Irina Pulyakhina Yavuz Ariyurek Ken Kraaijeveld Johan T den Dunnen Peter de Knijff Peter AC ’t Hoen Jeroen FJ Laros |
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| Institution: | .Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands ;.Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands ;.Department of Ecological Science, VU University Amsterdam, Amsterdam, The Netherlands ;.Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands |
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| Abstract: | We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-014-0555-3) contains supplementary material, which is available to authorized users. |
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