Fast alignment and preprocessing of chromatin profiles with Chromap

As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and...

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Autores principales: Zhang, Haowen, Song, Li, Wang, Xiaotao, Cheng, Haoyu, Wang, Chenfei, Meyer, Clifford A., Liu, Tao, Tang, Ming, Aluru, Srinivas, Yue, Feng, Liu, X. Shirley, Li, Heng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589834/
https://www.ncbi.nlm.nih.gov/pubmed/34772935
http://dx.doi.org/10.1038/s41467-021-26865-w
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author Zhang, Haowen
Song, Li
Wang, Xiaotao
Cheng, Haoyu
Wang, Chenfei
Meyer, Clifford A.
Liu, Tao
Tang, Ming
Aluru, Srinivas
Yue, Feng
Liu, X. Shirley
Li, Heng
author_facet Zhang, Haowen
Song, Li
Wang, Xiaotao
Cheng, Haoyu
Wang, Chenfei
Meyer, Clifford A.
Liu, Tao
Tang, Ming
Aluru, Srinivas
Yue, Feng
Liu, X. Shirley
Li, Heng
author_sort Zhang, Haowen
collection PubMed
description As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.
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spelling pubmed-85898342021-11-15 Fast alignment and preprocessing of chromatin profiles with Chromap Zhang, Haowen Song, Li Wang, Xiaotao Cheng, Haoyu Wang, Chenfei Meyer, Clifford A. Liu, Tao Tang, Ming Aluru, Srinivas Yue, Feng Liu, X. Shirley Li, Heng Nat Commun Article As sequencing depth of chromatin studies continually grows deeper for sensitive profiling of regulatory elements or chromatin spatial structures, aligning and preprocessing of these sequencing data have become the bottleneck for analysis. Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles. Nature Publishing Group UK 2021-11-12 /pmc/articles/PMC8589834/ /pubmed/34772935 http://dx.doi.org/10.1038/s41467-021-26865-w Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Haowen
Song, Li
Wang, Xiaotao
Cheng, Haoyu
Wang, Chenfei
Meyer, Clifford A.
Liu, Tao
Tang, Ming
Aluru, Srinivas
Yue, Feng
Liu, X. Shirley
Li, Heng
Fast alignment and preprocessing of chromatin profiles with Chromap
title Fast alignment and preprocessing of chromatin profiles with Chromap
title_full Fast alignment and preprocessing of chromatin profiles with Chromap
title_fullStr Fast alignment and preprocessing of chromatin profiles with Chromap
title_full_unstemmed Fast alignment and preprocessing of chromatin profiles with Chromap
title_short Fast alignment and preprocessing of chromatin profiles with Chromap
title_sort fast alignment and preprocessing of chromatin profiles with chromap
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8589834/
https://www.ncbi.nlm.nih.gov/pubmed/34772935
http://dx.doi.org/10.1038/s41467-021-26865-w
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