High-Throughput Identification of Adapters in Single-Read Sequencing Data.

Biomolecules
Asan M S H MohideenIgor Babiak

Abstract

Sequencing datasets available in public repositories are already high in number, and their growth is exponential. Raw sequencing data files constitute a substantial portion of these data, and they need to be pre-processed for any downstream analyses. The removal of adapter sequences is the first essential step. Tools available for the automated detection of adapters in single-read sequencing protocol datasets have certain limitations. To explore these datasets, one needs to retrieve the information on adapter sequences from the methods sections of appropriate research articles. This can be time-consuming in metadata analyses. Moreover, not all research articles provide the information on adapter sequences. We have developed adapt_find, a tool that automates the process of adapter sequences identification in raw single-read sequencing datasets. We have verified adapt_find through testing a number of publicly available datasets. adapt_find secures a robust, reliable and high-throughput process across different sequencing technologies and various adapter designs. It does not need prior knowledge of the adapter sequences. We also produced associated tools: random_mer, for the detection of random N bases either on one or both termin...Continue Reading

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Nov 27, 2008·Nature Methods·Michael A QuailDaniel J Turner
Nov 11, 2010·Nucleic Acids Research·Rasko LeinonenUNKNOWN International Nucleotide Sequence Database Collaboration
Dec 15, 2010·Current Protocols in Bioinformatics·Ben Langmead
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Feb 8, 2014·BioTechniques·Steven R HeadPhillip Ordoukhanian
Nov 14, 2018·Bioinformatics·Shifu ChenJia Gu

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Datasets Mentioned

BETA
SRR578913
SRR953567
SRR578917
SRR997335

Methods Mentioned

BETA
PCR
Illumina sequencing
Ion

Software Mentioned

Sequence Alignment Map ( SAM )
pandas
numpy
R package fastqcr
find
bowtie
SRA run selector
randomer
sh
ILLUMINA

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