EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides

Celia Blanco, Samuel Verbanic, Burckhard Seelig, Irene A. Chen

Research output: Contribution to journalLetterpeer-review

Abstract

In vitro evolution is a well-established technique for the discovery of functional RNA and peptides. Increasingly, these experiments are analyzed by high-throughput sequencing (HTS) for both scientific and engineering objectives, but computational analysis of HTS data, particularly for peptide selections, can present a barrier to entry for experimentalists. We introduce EasyDIVER (Easy pre-processing and Dereplication of In Vitro Evolution Reads), a simple, user-friendly pipeline for processing high-throughput sequencing data from in vitro selections and directed evolution experiments. The pipeline takes as input raw, paired-end, demultiplexed Illumina read files. For each sample provided, EasyDIVER outputs a dereplicated list of unique nucleic acid and/or peptide sequences and their count reads.

Original languageEnglish (US)
Pages (from-to)477-481
Number of pages5
JournalJournal of Molecular Evolution
Volume88
Issue number6
DOIs
StatePublished - Aug 1 2020

Bibliographical note

Funding Information:
This work was supported by the Otis Williams Fund; the Simons Collaboration on the Origins of Life [Grant Number 340762 to B.S., 290356FY18 to I.C]; the US National Aeronautics and Space Administration [Grant Number NNX14AK29G to B.S., NNX16AJ32G to I.C.]; the NIH [GM108703 to B.S.]; and the NIH New Innovator Program [Grant Number DP2GM123457 to I.C.].

Keywords

  • Bioinformatics
  • High-throughput sequencing
  • In vitro evolution
  • SELEX
  • mRNA display

PubMed: MeSH publication types

  • Letter

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