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RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data

SUMMARY: Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various metrics have been established to explore this layer of information. However, limited compatibility with alignment tools, reference genome...

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Detalles Bibliográficos
Autores principales: Hetzel, Sara, Giesselmann, Pay, Reinert, Knut, Meissner, Alexander, Kretzmer, Helene
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8686677/
https://www.ncbi.nlm.nih.gov/pubmed/34601556
http://dx.doi.org/10.1093/bioinformatics/btab663
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author Hetzel, Sara
Giesselmann, Pay
Reinert, Knut
Meissner, Alexander
Kretzmer, Helene
author_facet Hetzel, Sara
Giesselmann, Pay
Reinert, Knut
Meissner, Alexander
Kretzmer, Helene
author_sort Hetzel, Sara
collection PubMed
description SUMMARY: Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various metrics have been established to explore this layer of information. However, limited compatibility with alignment tools, reference genomes or the measurements they provide present a bottleneck for most groups to routinely perform read-level analysis. To address this, we developed RLM, a fast and scalable tool for the computation of several frequently used read-level methylation statistics. RLM supports standard alignment tools, works independently of the reference genome and handles most sequencing experiment designs. RLM can process large input files with a billion reads in just a few hours on common workstations. AVAILABILITY AND IMPLEMENTATION: https://github.com/sarahet/RLM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-86866772021-12-21 RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data Hetzel, Sara Giesselmann, Pay Reinert, Knut Meissner, Alexander Kretzmer, Helene Bioinformatics Applications Notes SUMMARY: Bisulfite sequencing data provide value beyond the straightforward methylation assessment by analyzing single-read patterns. Over the past years, various metrics have been established to explore this layer of information. However, limited compatibility with alignment tools, reference genomes or the measurements they provide present a bottleneck for most groups to routinely perform read-level analysis. To address this, we developed RLM, a fast and scalable tool for the computation of several frequently used read-level methylation statistics. RLM supports standard alignment tools, works independently of the reference genome and handles most sequencing experiment designs. RLM can process large input files with a billion reads in just a few hours on common workstations. AVAILABILITY AND IMPLEMENTATION: https://github.com/sarahet/RLM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-10-02 /pmc/articles/PMC8686677/ /pubmed/34601556 http://dx.doi.org/10.1093/bioinformatics/btab663 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Hetzel, Sara
Giesselmann, Pay
Reinert, Knut
Meissner, Alexander
Kretzmer, Helene
RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title_full RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title_fullStr RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title_full_unstemmed RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title_short RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
title_sort rlm: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8686677/
https://www.ncbi.nlm.nih.gov/pubmed/34601556
http://dx.doi.org/10.1093/bioinformatics/btab663
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