Crate ARGenus 

ARGenus - Antibiotic Resistance Gene Detection with Genus Classification

A targeted assembly pipeline for detecting ARGs from metagenomic reads and classifying their source genus using flanking sequence analysis.

Modules

• seqio: FASTA/FASTQ file I/O with gzip support
• paf: PAF (Pairwise Alignment Format) parsing
• extender: K-mer based contig extension
• classifier: Genus classification using flanking sequences
• snp: SNP verification for point mutation ARGs
• arg_db: ARG reference database building (NCBI/CARD)
• flanking_db: Flanking sequence database building
• fdb: FDB format compression and indexing
• flanking_db_ntprok: 5000bp flanking database building (nt_prok-based)

Modules

arg_db

ARG Reference Database Builder Module

classifier

Genus Classifier Module

extender

Contig Extender Module

fdb

FDB (Flanking Database) Format Module

flanking_db

Flanking Database Builder Module

flanking_db_ntprok

nt_prok-based 5000bp Flanking Database Builder

paf

PAF (Pairwise mApping Format) Parser Module

seqio

Sequence I/O Module

snp

SNP Verification Module