nanoSweet

Version

2.0.0

Demultiplex your nanopore (or other) reads! nanomux fuzzy matching useful for noisy reads. Written entirely in C.

In the repo, you can also find nanotrim – a small threaded program which you can use to filter out reads with a mean quality and between length between min and max.

Experimental - The repo contains nanodup – a small threaded program to deduplicate all the reads and saving information about duplication status.

Quick Start

$ git clone https://github.com/willros/nanoSweet.git
$ cd nanoSweet/
$ cc -o nob nob.c
$ ./nob

test nanomux

To get the help message, run ./nanomux:

    -b
        Path to barcode file (MANDATORY)
        Default: 
    -f
        Path to fastq file (MANDATORY)
        Default: 
    -o
        Name of output folder (MANDATORY)
        Default: 
    -p
        Position of barcode
        Default: 50
    -k
        Number of mismatches allowed
        Default: 0
    -t
        Trim reads from adapters or not
    -j
        Number of threads to use
        Default: 1
    -help
        Print this help to stdout and exit with 0
    -v
        Print the current version

Simple test command:

./nanomux -b tests/bc_test.csv -f tests/test.fastq -o TEST_NANOMUX -p 100 -k 1 -j 4 -t 

The barcode file MUST look like this:

# DUAL BARCODE EXAMPLE
name,forward,reverse
barcode1,ACTATCTACTA,GAGCATGTCGTA
barcode2,AGCGTATGCTGGTA,AGCATGCTATCG

# SINGLE BARCODE EXAMPLE
name,forward
barcode1,ACTATCTACTA
barcode2,AGCGTATGCTGGTA

test nanotrim

To get the help message, run ./nanotrim:

    -f
        Path to input folder or file (MANDATORY)
        Default: 
    -o
        Name of output folder (MANDATORY)
        Default: 
    -r
        Minimum read length
        Default: 0
    -R
        Maximum read length
        Default: 1000000
    -q
        Minimum quality
        Default: 0
    -j
        Number of threads to use
        Default: 1
    -help
        Print this help to stdout and exit with 0
    -v
        Print the current version

Simple test command:

./nanotrim -f tests/test.fastq -o TEST_NANOTRIM -r 100 -R 2000 -q 15 

How to cite

If you use nanoSweet or any of its tools in your research, please cite:

Rosenbaum W, Rubio Garcia M, Löfgren-Burström A, Larsson P, Edin S, Bronnec V, Palmqvist R. Full-length 16S rRNA nanopore sequencing enables species resolution of Fusobacterium associated with colorectal cancer. Gut Microbes. 2026;18(1):2656004. https://doi.org/10.1080/19490976.2026.2656004

Credit

nanoSweet uses kseq.h for fastq parsing, and nob.h, written by @tsoding, for overall useful functions!
It also uses thpool.h by Johan Hanssen Seferidis.

Change

• 2025-11-07
  • nanomux uses read buffer to process reads now. It does not read all reads into memory anymore.
  • added common.h for shared functions and structures.