Crate skesa_rs 

skesa-rs

Rust port of NCBI’s SKESA genome assembler.

This crate provides both a command-line interface and a library API for de-novo assembly of microbial genomes from short reads.

Library Usage

use skesa_rs::read_holder::ReadHolder;
use skesa_rs::sorted_counter;
use skesa_rs::graph_digger::{self, DiggerParams};

// Load reads into a ReadHolder
let mut reads = ReadHolder::new(false);
reads.push_back_str("ACGTACGTACGTACGTACGTACGT");

// Or load from files
let rg = skesa_rs::reads_getter::ReadsGetter::new(
    &["reads.fasta".to_string()], false
).unwrap();

// Count k-mers
let mut kmers = sorted_counter::count_kmers_sorted(
    rg.reads(), 21, 2, 32,
);
sorted_counter::get_branches(&mut kmers, 21);

// Assemble
let contigs = graph_digger::assemble_contigs(
    &mut kmers, 21, &DiggerParams::default(),
);

Modules

api

High-level builder API for embedding skesa-rs as a library.

assembler

assembly_stats

Assembly statistics and quality metrics.

bloom_filter

clean_reads

concurrent_hash

contig

contig_output

counter

db_graph

flat_counter

genetic_code

NCBI genetic code tables for codon-to-amino-acid translation. Port of SKESA’s genetic_code.hpp.

gfa

glb_align

Sequence alignment and distance utilities. Partial Rust implementation of SKESA’s glb_align.hpp/glb_align.cpp behavior.

graph_digger

graph_io

guided_assembly

guided_graph

guided_path

hash_graph_output

histogram

Histogram analysis utilities for k-mer count distributions. Port of FindValleyAndPeak, HistogramRange, GetAverageCount, CalculateGenomeSize from common_util.hpp.

kmer

kmer_counter

kmer_lookup

kmer_output

large_int

linked_contig

model

Nucleotide complement, IUPAC ambiguity codes, and related utilities. Port of SKESA’s Model.hpp.

nuc_prot_align

output

paired_reads

read_holder

reads_getter

rlimit

Optional address-space cap for development and testing.

snp_discovery

SNP discovery at fork points during graph traversal.

sorted_counter

spider_graph

untranslated

Skeleton stubs for C++ SKESA functions not yet translated to Rust.