BayesHammer: Bayesian Clustering for Error Correction in Single-cell Sequencing

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2013 Feb 2

PMID 23368723

Citations 225

Authors

Sergey I Nikolenko

Anton I Korobeynikov

Max A Alekseyev

Affiliations

Soon will be listed here.

Abstract

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.

Citing Articles

Combining Short- and Long-Read Transcriptomes for Targeted Enzyme Discovery.

Jutersek M, Petek M, Baebler S Methods Mol Biol. 2025; 2880:69-99.

PMID: 39900755 DOI: 10.1007/978-1-0716-4276-4_4.

A respiro-fermentative strategy to survive nanoxia in Acidobacterium capsulatum.

Trojan D, Garcia-Robledo E, Hausmann B, Revsbech N, Woebken D, Eichorst S FEMS Microbiol Ecol. 2024; 100(12).

PMID: 39557655 PMC: 11636273. DOI: 10.1093/femsec/fiae152.

Unveiling interactions mediated by B vitamins between diatoms and their associated bacteria from cocultures.

Costas-Selas C, Martinez-Garcia S, Pinhassi J, Fernandez E, Teira E J Phycol. 2024; 60(6):1456-1470.

PMID: 39413213 PMC: 11670299. DOI: 10.1111/jpy.13515.

Dataset of 16S rRNA gene sequences of 111 healthy and Newcastle disease infected caecal samples from multiple chicken breeds of Pakistan.

Ameer A, Saleem F, Keating C, Gundogdu O, Zeeshan Ijaz U, Javed S Data Brief. 2024; 57:110957.

PMID: 39386325 PMC: 11461973. DOI: 10.1016/j.dib.2024.110957.

Whole genome sequence data of a lignocellulose-degrading bacterium, Arthrobacter koreensis BSB isolated from the soils of Santiniketan, India.

Show B, Ross A, Biswas R, Chaudhury S, Balachandran S Data Brief. 2024; 57:110915.

PMID: 39328963 PMC: 11424791. DOI: 10.1016/j.dib.2024.110915.

References

Chaisson M, Pevzner P . Short read fragment assembly of bacterial genomes. Genome Res. 2007; 18(2):324-30. PMC: 2203630. DOI: 10.1101/gr.7088808. View

Hamady M, Knight R . Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 2009; 19(7):1141-52. PMC: 3776646. DOI: 10.1101/gr.085464.108. View

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

Gurevich A, Saveliev V, Vyahhi N, Tesler G . QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29(8):1072-5. PMC: 3624806. DOI: 10.1093/bioinformatics/btt086. View

Grindberg R, Ishoey T, Brinza D, Esquenazi E, Coates R, Liu W . Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One. 2011; 6(4):e18565. PMC: 3075265. DOI: 10.1371/journal.pone.0018565. View

Roberts M, Hayes W, Hunt B, Mount S, Yorke J . Reducing storage requirements for biological sequence comparison. Bioinformatics. 2004; 20(18):3363-9. DOI: 10.1093/bioinformatics/bth408. View

Gill S, Pop M, DeBoy R, Eckburg P, Turnbaugh P, Samuel B . Metagenomic analysis of the human distal gut microbiome. Science. 2006; 312(5778):1355-9. PMC: 3027896. DOI: 10.1126/science.1124234. View

Cock P, Fields C, Goto N, Heuer M, Rice P . The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009; 38(6):1767-71. PMC: 2847217. DOI: 10.1093/nar/gkp1137. View

Chitsaz H, Yee-Greenbaum J, Tesler G, Lombardo M, Dupont C, Badger J . Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol. 2011; 29(10):915-21. PMC: 3558281. DOI: 10.1038/nbt.1966. View

10.

Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken R . Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol. 2008; 11(3):198-204. PMC: 3635501. DOI: 10.1016/j.mib.2008.05.006. View

11.

Li J, Vederas J . Drug discovery and natural products: end of an era or an endless frontier?. Science. 2009; 325(5937):161-5. DOI: 10.1126/science.1168243. View

12.

Medvedev P, Scott E, Kakaradov B, Pevzner P . Error correction of high-throughput sequencing datasets with non-uniform coverage. Bioinformatics. 2011; 27(13):i137-41. PMC: 3117386. DOI: 10.1093/bioinformatics/btr208. View

13.

Kelley D, Schatz M, Salzberg S . Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 2010; 11(11):R116. PMC: 3156955. DOI: 10.1186/gb-2010-11-11-r116. View