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Published June 14, 2024 | Published
Journal Article Open

Flexible parsing, interpretation, and editing of technical sequences with splitcode

  • 1. ROR icon California Institute of Technology

Abstract

Motivation

Next-generation sequencing libraries are constructed with numerous synthetic constructs such as sequencing adapters, barcodes, and unique molecular identifiers. Such sequences can be essential for interpreting results of sequencing assays, and when they contain information pertinent to an experiment, they must be processed and analyzed.

Results

We present a tool called splitcode, that enables flexible and efficient parsing, interpreting, and editing of sequencing reads. This versatile tool facilitates simple, reproducible preprocessing of reads from libraries constructed for a large array of single-cell and bulk sequencing assays.

Availability

The splitcode program is free, open source, and available for download at http://github.com/pachterlab/splitcode.

Supplementary information

Supplementary data are available at Bioinformatics online.

Copyright and License

Funding

D.K.S. was funded by the UCLA-Caltech Medical Scientist Training Program (NIH NIGMS training grant T32 GM008042). L.P. was supported in part by the National Institutes of Health (NIH) grants U19MH114830 and 5UM1HG012077-02.

Conflict of Interest

none declared

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Additional details

Created:
June 25, 2024
Modified:
June 25, 2024