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PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets

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799 days ago
PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets https://t.co/VPacDWgBP7 https://t.co/PehJgZKCOj
RT @CompBiolPapers: PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets https:…
PRINSEQ++, a multi-threaded tool for fast and efficient quality control and preprocessing of sequencing datasets https://t.co/sX9TAeQYdB
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Supplemental Information

Raw data for timing experiment

Each row is a timing measurement for some input size/ number of threads combination

DOI: 10.7287/peerj.preprints.27553v1/supp-1

Summary statistics used to plot figure 1

Each rows indicates the average time, standard deviation, standard error, and .95 confidence interval for the timing measurements for each input size/number of threads combination. This data is derived from sup_table1

DOI: 10.7287/peerj.preprints.27553v1/supp-2

Code to plot figure1

jupyter notebook of the code used to plot figure1. This is also available in the github repository

DOI: 10.7287/peerj.preprints.27553v1/supp-3

Runtime comparison, Run-time of prinseq-lite and PRINSEQ++ was measured on several FASTQ pair files of different sizes with equivalent options. PRINSEQ++ was run with different number of threads, prinseq-lite single-threaded. Mean speedup of PRINSEQ++ ove

DOI: 10.7287/peerj.preprints.27553v1/supp-4

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vito Adrian Cantu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Jeffrey Sadural conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Robert Edwards conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

https://github.com/Adrian-Cantu/PRINSEQ-plus-plus

Funding

VAC and JS were supported by NSF grant number MCB-1441985 to RE; Department of Energy Lawrence Livermore National Laboratory grant B618146 to RE; computational resources were supported by NSF grant DBI-0850356 to RE. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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