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.
Bibliographical noteFunding 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.].
© 2020, The Author(s).
- High-throughput sequencing
- In vitro evolution
- mRNA display
PubMed: MeSH publication types
- Research Support, Non-U.S. Gov't
- Research Support, U.S. Gov't, Non-P.H.S.
- Research Support, N.I.H., Extramural