The FASTQ+ format and PISA

Research output: Contribution to journalJournal articlepeer-review

Standard

The FASTQ+ format and PISA. / Shi, Quan; Liu, Shiping; Kristiansen, Karsten; Liu, Longqi.

In: Bioinformatics, Vol. 38, No. 19, 2022, p. 4639-4642.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Shi, Q, Liu, S, Kristiansen, K & Liu, L 2022, 'The FASTQ+ format and PISA', Bioinformatics, vol. 38, no. 19, pp. 4639-4642. https://doi.org/10.1093/bioinformatics/btac562

APA

Shi, Q., Liu, S., Kristiansen, K., & Liu, L. (2022). The FASTQ+ format and PISA. Bioinformatics, 38(19), 4639-4642. https://doi.org/10.1093/bioinformatics/btac562

Vancouver

Shi Q, Liu S, Kristiansen K, Liu L. The FASTQ+ format and PISA. Bioinformatics. 2022;38(19):4639-4642. https://doi.org/10.1093/bioinformatics/btac562

Author

Shi, Quan ; Liu, Shiping ; Kristiansen, Karsten ; Liu, Longqi. / The FASTQ+ format and PISA. In: Bioinformatics. 2022 ; Vol. 38, No. 19. pp. 4639-4642.

Bibtex

@article{f777513cadfa453988a4d23882a7ed4c,
title = "The FASTQ+ format and PISA",
abstract = "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/CRAMformat 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/PISAContact: liulongqi@genomics.cn or kk@bio.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.",
author = "Quan Shi and Shiping Liu and Karsten Kristiansen and Longqi Liu",
year = "2022",
doi = "10.1093/bioinformatics/btac562",
language = "English",
volume = "38",
pages = "4639--4642",
journal = "Bioinformatics (Online)",
issn = "1367-4811",
publisher = "Oxford University Press",
number = "19",

}

RIS

TY - JOUR

T1 - The FASTQ+ format and PISA

AU - Shi, Quan

AU - Liu, Shiping

AU - Kristiansen, Karsten

AU - Liu, Longqi

PY - 2022

Y1 - 2022

N2 - 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/CRAMformat 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/PISAContact: liulongqi@genomics.cn or kk@bio.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.

AB - 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/CRAMformat 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/PISAContact: liulongqi@genomics.cn or kk@bio.ku.dkSupplementary information: Supplementary data are available at Bioinformatics online.

U2 - 10.1093/bioinformatics/btac562

DO - 10.1093/bioinformatics/btac562

M3 - Journal article

C2 - 35993907

VL - 38

SP - 4639

EP - 4642

JO - Bioinformatics (Online)

JF - Bioinformatics (Online)

SN - 1367-4811

IS - 19

ER -

ID: 322871829