HFKReads

An ultra-fast and efficient tool for high frequency kmer sequencing reads extraction

1. Install

(1) Pre-built binaries for x86_64 Linux

wget -c https://github.com/HuiyangYu/HFKReads/releases/download/v2.04/HFKReads-2.04-Linux-x86_64.tar.gz
tar zvxf HFKReads-2.04-Linux-x86_64.tar.gz
cd HFKReads-2.04-Linux-x86_64
./hfkreads -h

If the pre-built binaries are not functional, you need to install from the source code.

(2) Building from source code （Linux or Mac）

git clone https://github.com/HuiyangYu/HFKReads.git
cd HFKReads
make
cd bin
./hfkreads -h

2. Usage

Usage: hfkreads -1 PE1.fq.gz -2 PE2.fq.gz -o OutPrefix
 Input/Output options:
   -1	<str>   paired-end fasta/q file1
   -2	<str>   paired-end fasta/q file2
   -s	<str>   single-end fasta/q file
   -o	<str>   prefix of output file
 Filter options:
   -b	<int>   min base quality [0]
   -q	<int>   min average base quality [20]
   -l	<int>   min length of read [half]
   -r	<float> max unknown base (N) ratio [0.1]
   -k	<int>   kmer length [31]
   -w	<int>   minimizer window size [10]
   -m	<int>   min count for high frequency kmer (HFK) [3] 
   -x	<float>	min ratio of HFK in the read [0.9]
   -n	<int>   read number to use [1000000]
   -a	        use all the read
 Other options:
   -d           drop the duplicated reads/pairs
   -f           output the kmer frequency file
   -A           keep base quality in output
   -t           number of threads [1]
   -h           show help [v2.04]

3. Example

3.1 Extracting high-frequency k-mer reads from paired-end short reads

hfkreads -1 PE_1.fq.gz -2 PE_2.fq.gz -o test1

The output files consist of four files:
test1_pe_1.fa
test1_pe_2.fa
test1_se_1.fa
test1_se_2.fa
The output file with the 'se' label are unpaired high-frequency k-mer reads.

3.2 Extracting high-frequency k-mer reads from single-end short reads or long reads

hfkreads -s SE.fq.gz -o test2

The output result consists of a single file named "test2.fa".

3.3 Extracting high-quality reads without filtering the k-mers

hfkreads -1 PE_1.fq.gz -2 PE_2.fq.gz -m 1 -o test3
hfkreads -s SE.fq.gz -m 1 -o test4

To filter out low-quality reads only, the default '-m 3' parameter should change to '-m 1'.

4. License

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This project is licensed under the GPL-3.0 license - see the LICENSE file for details