Dataset Information

AdapterRemoval: easy cleaning of next-generation sequencing reads.

ABSTRACT: BACKGROUND:With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses. FINDINGS:We present a tool called AdapterRemoval which is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5' and 3' ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data. CONCLUSIONS:AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in terms of sensitivity and specificity. AdapterRemoval has already been used in various large projects and it is possible to extend it further to accommodate application-specific biases in the data.

SUBMITTER: Lindgreen S

PROVIDER: S-EPMC3532080 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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AdapterRemoval: easy cleaning of next-generation sequencing reads.

Lindgreen Stinus S

BMC research notes 20120702

<h4>Background</h4>With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses.<h4>Findings</h4>We present a tool called AdapterRemoval which i ...[more]

PMID: 22748135

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Project description:BackgroundWith the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate "ready-to-align" datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output).MethodsECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC-Irb-SSC-IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses.ResultsECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC-Irb-SSC-IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%.ConclusionsECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/.

Dataset Information

AdapterRemoval: easy cleaning of next-generation sequencing reads.

Publications

AdapterRemoval: easy cleaning of next-generation sequencing reads.

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