About us
Support is provided at the Contact, GitHub issues, GitHub discussions or by email.
For support requests it is usually helpful if you provide details about your data (size and type of sequences) and your execution environment (CPU cores, RAM, operating system).
Community feedback and feature requests are also appreciated.
🤵 PhaBOX Team
Head of PhaBOX program| Jiayu SHANG | Cheng PENG |
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| Yanni SUN |
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🤵🤵 Yanni's Group
Our groupmates also provide many useful tools for bioinformatics analysis. Below are our recent publications. Hope they help you!
Tools for Virus
VirStrain (2022) Paper Code
VirStrain is a computational tool for identifying viral strains from short-read sequencing data...
RVHaplo (2022) Paper Code
RVHaplo is a tool for reconstructing viral haplotypes from long reads...
HaploDMF (2022) Paper Code
HaploDMF is a tool for reconstructing viral haplotypes from long reads...
PhaGenus (2023) Paper Code
PhaGenus is a learning-based model that conducts genus-level taxonomic classification for phage contigs...
ViralM (2024) Code
A Viral Language Model for virus identification from metagenomic data.
VirBot (2023) Paper Code
VirBot is an easy-to-use yet effective tool for identifying RNA viruses from metagenomic data...
SegVir (2024) Paper Code
SegVir is designed to identify and reconstruct complete genomes of segmented RNA viruses...
RdRpBin (2022) Paper Code
RdRpBin can identify and classify the RNA virus reads in metagenomic data...
Tools for Plasmid
PLASMe (2023) Paper Code
PLASMe is a tool to identify plasmid contigs from short-read assemblies using the Transformer...
HOTSPOT (2023) Paper Code
HOTSPOT is a deep learning tool based on the Transformer model, specifically designed for predicting the hosts of plasmids...
Tools for Bacteria
StrainScan (2023) Paper Code
StrainScan is an efficient, accurate, and high-resolution tool for bacterial strain-level composition analysis...
Other tools
SourceID-NMF (2024) Paper Code
SourceID-NMF is a microbial source tracking tool...
RTTAP Code
RTTAP (Read-based Total-infectome Taxonomic Analysis Pipeline) is a fast, accurate, and sensitive pipeline focusing analyses of the total-infectome of clinical metatranscriptomic data...