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GTDB-based packages enhance GraftM performance

Korzhenkov, A. A.

2023-10-05 bioinformatics
10.1101/2023.10.03.560708 bioRxiv
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In this short note I present a way to enhance GraftM performance and incorporate novel genome-based prokaryotic taxonomy to sequencing data classification.

Matching journals

The top 5 journals account for 50% of the predicted probability mass.

1
PeerJ
◐ 308 papers in training set
Top 0.1%
18.8%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 1%
18.8%
Similar papers in this journal
3
BMC Bioinformatics
○ 457 papers in training set
Top 0.9%
8.0%
Similar papers in this journal
4
Frontiers in Microbiology
○ 427 papers in training set
Top 3%
4.1%
Similar papers in this journal
5
mSystems
● 394 papers in training set
Top 2%
4.1%
Similar papers in this journal
50% of probability mass above
6
F1000Research
○ 88 papers in training set
Top 0.5%
3.3%
7
PLOS ONE
● 5266 papers in training set
Top 38%
2.8%
8
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
2.7%
9
Microorganisms
○ 106 papers in training set
Top 0.8%
2.7%
10
Molecular Ecology Resources
○ 171 papers in training set
Top 1%
2.1%
11
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
1.7%
12
GigaScience
◐ 212 papers in training set
Top 2%
1.7%
13
Scientific Reports
○ 3612 papers in training set
Top 56%
1.5%
14
BMC Genomics
○ 406 papers in training set
Top 5%
1.5%
15
Frontiers in Bioinformatics
○ 49 papers in training set
Top 0.8%
1.1%
16
Briefings in Bioinformatics
◐ 354 papers in training set
Top 6%
1.1%
17
Environmental Microbiome
○ 29 papers in training set
Top 0.5%
1.1%
18
Genes
○ 144 papers in training set
Top 3%
1.1%
19
Metabarcoding and Metagenomics
● 14 papers in training set
Top 0.2%
1.1%
20
Journal of Open Source Software
● 25 papers in training set
Top 0.3%
1.1%
21
Microbiology Spectrum
● 469 papers in training set
Top 9%
1.1%
22
Microbial Genomics
● 225 papers in training set
Top 2%
1.1%
23
Peer Community Journal
● 281 papers in training set
Top 5%
0.9%
24
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 6%
0.9%
25
mSphere
● 302 papers in training set
Top 7%
0.6%
26
BMC Research Notes
○ 33 papers in training set
Top 1%
0.6%
27
Microbiome
○ 154 papers in training set
Top 2%
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.