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

Journal of Molecular Evolution
Celia BlancoIrene A Chen

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.

References

Feb 1, 2011·Bioinformatics·Robert Schmieder, Robert Edwards
Feb 16, 2012·BMC Bioinformatics·Andre P MasellaJosh D Neufeld
Oct 22, 2013·Bioinformatics·Jiajie ZhangAlexandros Stamatakis
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Mar 4, 2015·Molecular Therapy. Nucleic Acids·Khalid K AlamDonald H Burke
Aug 9, 2017·Genome Biology·Alan F RubinDouglas M Fowler
Jul 10, 2018·Nucleic Acids Research·Nam Nguyen QuangFrédéric Ducongé
Jan 3, 2019·Annual Review of Biophysics·Celia BlancoIrene A Chen
Feb 10, 2019·Methods : a Companion to Methods in Enzymology·Yohei Yokobayashi
Jan 1, 2020·ACS Synthetic Biology·Matilda S NewtonBurckhard Seelig
Jan 23, 2020·Physical Chemistry Chemical Physics : PCCP·Celia BlancoIrene A Chen

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Citations

May 19, 2021·Proceedings of the National Academy of Sciences of the United States of America·Yei-Chen LaiIrene A Chen
Jun 25, 2021·Chemical Society Reviews·Golnaz KamaliniaRichard W Roberts
Sep 12, 2021·Scientific Reports·Nisha KanwarBurckhard Seelig

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Methods Mentioned

BETA
PCR
Illumina sequencing

Software Mentioned

- Toolkit
fastas
fastqs
fastq
EasyDIVER
FASTX
Python
PANDAseq

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