The FASTQ+ format and PISA
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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 journal › Journal article › peer-review
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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