The FASTQ+ format and PISA

Quan Shi; Shiping Liu; Karsten Kristiansen; Longqi Liu

doi:10.1093/bioinformatics/btac562

The FASTQ+ format and PISA

Bioinformatics. 2022 Sep 30;38(19):4639-4642. doi: 10.1093/bioinformatics/btac562.

Authors

Quan Shi^{1

2}, Shiping Liu¹, Karsten Kristiansen^{1

2

3}, Longqi Liu¹

Affiliations

¹ BGI-Shenzhen, Shenzhen 518103, China.
² Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark.
³ Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 166555, P. R. China.

PMID: 35993907
DOI: 10.1093/bioinformatics/btac562

Abstract

Summary: The FASTQ+ format is designed for single-cell experiments. It extends various optional tags, including cell barcodes and unique molecular identifiers, to the sequence identifier and is fully compatible with the FASTQ format. In addition, PISA implements various utilities for processing sequences in the FASTQ format and alignments in the SAM/BAM/CRAM format from single-cell experiments, such as converting FASTQ format to FASTQ+, annotating alignments, PCR deduplication, feature counting and barcodes correction. The software is open-source and written in C language.

Availability and implementation: https://doi.org/10.5281/zenodo.7007056 or https://github.com/shiquan/PISA.

Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

Language*
Polymerase Chain Reaction
Sequence Analysis, DNA
Software*