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.
$ git clone https://github.com/willros/nanoSweet.git
$ cd nanoSweet/
$ cc -o nob nob.c
$ ./nobTo 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 versionSimple 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
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 versionSimple test command:
./nanotrim -f tests/test.fastq -o TEST_NANOTRIM -r 100 -R 2000 -q 15 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.
- 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.