Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets, BMC Bioinformatics
Por um escritor misterioso
Last updated 25 abril 2025

Background Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates. Results Our results show that long-read classifiers generally performed best. Several short-read classification and profiling methods produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, two long-read methods (BugSeq, MEGAN-LR & DIAMOND) and one generalized method (sourmash) displayed high precision and recall without any filtering required. Furthermore, in the PacBio HiFi datasets these methods detected all species down to the 0.1% abundance level with high precision. Some long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to resemble the precision and recall of the top-performing methods. We found read quality affected performance for methods relying on protein prediction or exact k-mer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (< 2 kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for classification methods, we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing. Conclusions Our critical assessment of available methods provides best-practice recommendations for current research using long reads and establishes a baseline for future benchmarking studies.

Evaluation of taxonomic classification and profiling methods for

UMGAP: the Unipept MetaGenomics Analysis Pipeline

IJMS, Free Full-Text

Frontiers Evaluation of the Microba Community Profiler for

The effect of taxonomic classification by full-length 16S rRNA

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow

Short- and long-read metagenomics expand individualized structural

Figure 2 from An introduction to the analysis of shotgun

Shotgun metagenomics

PDF) Evaluation of taxonomic classification and profiling methods

Impact of sequencing depth on the characterization of the
Best-practice protocol for the acquisition and analysis of
Recomendado para você
-
Roblox Adopt Me Trading Values - Tips to Get Rich25 abril 2025
-
Trade Roblox Murder Mystery 2 Items25 abril 2025
-
RoValk - The Roblox Trading Addon25 abril 2025
-
MM2 Gold Vampire's Edge is worth?!…25 abril 2025
-
Total-Debt-to-Total-Assets Ratio: Meaning, Formula, and What's Good25 abril 2025
-
MM2 Small Set (Full - 103pcs Item) - Roblox Murder Mystery 2, Video Gaming, Video Games, Others on Carousell25 abril 2025
-
Trading junk, READ THE ENTIRE POST25 abril 2025
-
TRADING CARD GAME UNION ARENA [UA03BT] HUNTER×HUNTER cards list25 abril 2025
-
how much value is chroma lightbringer mm2|TikTok Search25 abril 2025
-
♕ 𝚔𝚎𝚍𝚎𝚖 ♕ on X: trading laser, for laser and something else. Check mm2 values! The higher laser is what I'm trading xx #mm2trading #mm2 #trading / X25 abril 2025
você pode gostar
-
Assista ao Trailer da Série HALO25 abril 2025
-
Casa Da Barbie Infantil Rosa 36 Móveis E Brinde25 abril 2025
-
Play Lemmings 2: The Tribes online25 abril 2025
-
Download do APK de Gacha Club Clothes ideas para Android25 abril 2025
-
Bucie is ready for her Rebirth25 abril 2025
-
As 7 gerações dos hokages de konoha.. desenho lindo demais25 abril 2025
-
Printable Back to School Sign/ De Vuelta a La Escuela25 abril 2025
-
Data de lançamento da 3° temporada de Demon Slayer - Arco dos Ferreiro25 abril 2025
-
Podcast:AMN Anime Championship Tournament Round 2 - Tohsaka Rin vs25 abril 2025
-
2023 Soft TPU Anime Jujutsu Phone Case Silicone Cover For Infinix Note 30i 30 Pro 4G 30 VIP Spark 10C 10 GO 2023 Smart 7 HD25 abril 2025