LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data
While several well-established quality control (QC) tools exist for short-read sequencing data, there is a general paucity of computational tools that efficiently deliver comprehensive metrics across a wide range of long-read sequencing data formats, such as Oxford Nanopore (ONT) POD5, ONT FAST5, ON...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025000182 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832573231390785536 |
|---|---|
| author | Jonathan Elliot Perdomo Mian Umair Ahsan Qian Liu Li Fang Kai Wang |
| author_facet | Jonathan Elliot Perdomo Mian Umair Ahsan Qian Liu Li Fang Kai Wang |
| author_sort | Jonathan Elliot Perdomo |
| collection | DOAJ |
| description | While several well-established quality control (QC) tools exist for short-read sequencing data, there is a general paucity of computational tools that efficiently deliver comprehensive metrics across a wide range of long-read sequencing data formats, such as Oxford Nanopore (ONT) POD5, ONT FAST5, ONT basecall summary, Pacific Biosciences (PacBio) unaligned BAM, and Illumina Complete Long Read (ICLR) FASTQ file formats. In addition to nucleotide sequence information, some file formats such as POD5 contain raw signal information used for base calling, while other file formats such as aligned BAM contain alignments to a linear reference genome or transcriptome and may also contain base modification information. There is currently no single available QC tool capable of summarizing each of these features. Furthermore, high-performance tools are required to efficiently process the growing data volumes from long-read sequencing platforms. To address these challenges, here we present LongReadSum, a high-performance tool for generating a summary QC report for major types of long-read sequencing data. We also demonstrate a few examples using LongReadSum to analyze cDNA sequencing, direct RNA sequencing, ONT reduced representation methylation sequencing (RRMS), and whole genome sequencing (WGS) data. |
| format | Article |
| id | doaj-art-9881aee34d0944f385f01b02855c03b8 |
| institution | Kabale University |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-9881aee34d0944f385f01b02855c03b82025-02-02T05:27:03ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-0127556563LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing dataJonathan Elliot Perdomo0Mian Umair Ahsan1Qian Liu2Li Fang3Kai Wang4Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USARaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USARaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USARaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USARaymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA; Corresponding author.While several well-established quality control (QC) tools exist for short-read sequencing data, there is a general paucity of computational tools that efficiently deliver comprehensive metrics across a wide range of long-read sequencing data formats, such as Oxford Nanopore (ONT) POD5, ONT FAST5, ONT basecall summary, Pacific Biosciences (PacBio) unaligned BAM, and Illumina Complete Long Read (ICLR) FASTQ file formats. In addition to nucleotide sequence information, some file formats such as POD5 contain raw signal information used for base calling, while other file formats such as aligned BAM contain alignments to a linear reference genome or transcriptome and may also contain base modification information. There is currently no single available QC tool capable of summarizing each of these features. Furthermore, high-performance tools are required to efficiently process the growing data volumes from long-read sequencing platforms. To address these challenges, here we present LongReadSum, a high-performance tool for generating a summary QC report for major types of long-read sequencing data. We also demonstrate a few examples using LongReadSum to analyze cDNA sequencing, direct RNA sequencing, ONT reduced representation methylation sequencing (RRMS), and whole genome sequencing (WGS) data.http://www.sciencedirect.com/science/article/pii/S2001037025000182Quality controlLong-read sequencing |
| spellingShingle | Jonathan Elliot Perdomo Mian Umair Ahsan Qian Liu Li Fang Kai Wang LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data Computational and Structural Biotechnology Journal Quality control Long-read sequencing |
| title | LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data |
| title_full | LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data |
| title_fullStr | LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data |
| title_full_unstemmed | LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data |
| title_short | LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data |
| title_sort | longreadsum a fast and flexible quality control and signal summarization tool for long read sequencing data |
| topic | Quality control Long-read sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025000182 |
| work_keys_str_mv | AT jonathanelliotperdomo longreadsumafastandflexiblequalitycontrolandsignalsummarizationtoolforlongreadsequencingdata AT mianumairahsan longreadsumafastandflexiblequalitycontrolandsignalsummarizationtoolforlongreadsequencingdata AT qianliu longreadsumafastandflexiblequalitycontrolandsignalsummarizationtoolforlongreadsequencingdata AT lifang longreadsumafastandflexiblequalitycontrolandsignalsummarizationtoolforlongreadsequencingdata AT kaiwang longreadsumafastandflexiblequalitycontrolandsignalsummarizationtoolforlongreadsequencingdata |