Back

The Precise Basecalling of Short-Read Nanopore Sequencing

Wang, Z.; Tu, M.-J.; Song, C.; Liu, Z.; Wang, K. K.; Chen, S.; Yu, A.-M.; DING, H.

2024-09-17 bioinformatics
10.1101/2024.09.12.612746 bioRxiv
Show abstract

The nanopore sequencing of short sequences, whose lengths are typically less than 0.3kb therefore comparable with Illumina sequencing techniques, has recently gained wide attention. Here, we design a scheme for training nanopore basecallers that are specialized for short biomolecules. With bioengineered RNA (BioRNA) molecules as examples, we demonstrate the superior accuracy of basecallers trained by our scheme.

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
Nature Communications
○ 5641 papers in training set
Top 4%
27.2%
Similar papers in this journal
2
Nature Biotechnology
○ 172 papers in training set
Top 0.1%
13.2%
Similar papers in this journal
3
Nature Methods
○ 385 papers in training set
Top 1%
7.5%
Similar papers in this journal
4
Nucleic Acids Research
◐ 1281 papers in training set
Top 4%
5.0%
Similar papers in this journal
50% of probability mass above
5
Molecular Therapy - Nucleic Acids
○ 25 papers in training set
Top 0.1%
3.3%
Similar papers in this journal
6
Molecular Therapy Nucleic Acids
○ 39 papers in training set
Top 0.2%
3.3%
7
Genome Biology
○ 637 papers in training set
Top 4%
3.3%
8
Science Advances
● 1243 papers in training set
Top 12%
2.8%
9
Proceedings of the National Academy of Sciences
● 2444 papers in training set
Top 19%
2.7%
10
RNA Biology
○ 78 papers in training set
Top 0.6%
1.8%
11
Cell Reports Methods
○ 165 papers in training set
Top 2%
1.5%
12
Advanced Science
○ 286 papers in training set
Top 6%
1.4%
13
Analytical Chemistry
● 218 papers in training set
Top 2%
1.4%
14
Scientific Reports
○ 3612 papers in training set
Top 59%
1.4%
15
eLife
● 5828 papers in training set
Top 57%
1.2%
16
Nature Machine Intelligence
○ 70 papers in training set
Top 2%
1.2%
17
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
1.1%
18
Nature Biomedical Engineering
○ 47 papers in training set
Top 1%
1.1%
19
Nature Chemical Biology
○ 119 papers in training set
Top 2%
1.1%
20
RNA
● 189 papers in training set
Top 1%
0.9%
21
Molecular Therapy - Methods & Clinical Development
○ 38 papers in training set
Top 0.6%
0.9%
22
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.9%
23
Bioinformatics
◐ 1204 papers in training set
Top 8%
0.9%
24
iScience
○ 1154 papers in training set
Top 34%
0.9%
25
Communications Biology
○ 993 papers in training set
Top 28%
0.9%
26
Genome Research
● 468 papers in training set
Top 7%
0.6%
27
Cell Genomics
○ 172 papers in training set
Top 5%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.