willros / nanomux_c

nanomux_c

Demultiplex your nanopore (or other) reads! Implements fuzzy matching useful for noisy reads. Written entirely in C, so should compile on most platforms.

Quick Start

$ git clone https://github.com/willros/nanomux_c.git
$ cd nanomux_c/
$ chmod +x build.sh
$ ./build.sh 

# test nanomux
$ ./nanomux tests/bc_test.csv tests/test.fastq 600 2000 200 1 TEST_NANOMUX trim split 4

Information

The fastq parsing still runs in single threaded mode, hence it is quite slow. I will try do implement multithreading for this in the future.

Help

Just run ./nanomux to get the help message:

[USAGE] Add the following arguments in this exact order:
   ./nanomux
   <barcode_file: path>
   <fastq_file: path>
   <read_len_min: int>
   <read_len_max: int>
   <barcode_pos: int>
   <k: int>
   <output_folder: path>
   <trim_option: trim|notrim>
   <split_option: split|nosplit>
   <num_threads: int>

• barcode_pos: where to search for the barcode in the ends. if barcode_pos == 200 and the read length is 1000, the barcodes will be searched for from position 0 -> 200 and 800 -> 1000.
• k: allowed number of mismatches
• trim_option: To trim the reads to the left and right of the found barcode.
• split_option: Try to split reads longer than 2500 if an adapter sequence is found in the middle. One splitted read results in two new reads, with the suffix _1 and _2.

Usage

barcode_file.csv MUST have the follwing shape:

• columns:
  • name
  • forward barcode
  • reverse barcode

bc1,ATACGATGCTA,GTCGATGTCTGA
b2,GACACACAC,GTCGATTGATG
...

Credit

nanomux_c uses kseq.h for fastq parsing, and nob.h, written by @tsoding (Alexey Kutepov), for overall useful functions!

TODO

• trim barcodes
• multi threading
• read splitting
• [] multi threading for fastq parsing