argenus/lib.rs
1//! ARGenus - Antibiotic Resistance Gene Detection with Genus Classification
2//!
3//! A targeted assembly pipeline for detecting ARGs from metagenomic reads
4//! and classifying their source genus using flanking sequence analysis.
5//!
6//! # Modules
7//! - `seqio`: FASTA/FASTQ file I/O with gzip support
8//! - `paf`: PAF (Pairwise Alignment Format) parsing
9//! - `extender`: K-mer based contig extension
10//! - `classifier`: Genus classification using flanking sequences
11//! - `snp`: SNP verification for point mutation ARGs
12//! - `arg_db`: ARG reference database building (NCBI/CARD)
13//! - `flanking_db`: Flanking sequence database building
14//! - `fdb`: FDB format compression and indexing
15//! - `flanking_db_ntprok`: 5000bp flanking database building (nt_prok-based)
16
17pub mod seqio;
18pub mod paf;
19pub mod extender;
20pub mod classifier;
21pub mod snp;
22pub mod arg_db;
23pub mod flanking_db;
24pub mod fdb;
25pub mod flanking_db_ntprok;
26pub mod reassemble;