LongReadQC is a quality control tool for long reads. LongReadQC is written in C. LongReadQC is in development
LongReadQC currently has two functions:
- QC for fastq file. LongReadQC will generate a text file showing basic information of the input reads.
Usage: longreadqc fq [options]
Options:
-h, --help output this usage information
-i, --input_file path to the input file, which can be fasta, fastq or bam. Use this argument if only you have only one input file
-l, --input_list_file a file that contains the paths of all the input files. Usage this argument if you have multiple input files
-p, --out_prefix prefix of output files. (required)
-d, --out_dir output directory. (default: ./longreadqc_out/)
For example,
longreadqc fq -i FileName.fastq -d ./FileName_longreadqc_out/ -p sample01
longreadqc fq -l SampleName.fastqs.list -d ./SampleName_longreadqc_out/ -p sample02
- Filtering reads. LongReadQC will remove reads that are illegal, for example, reads that have different length in base and quality. Users can also set min_read_length and max_read_length to get the reads in the intended length.
Usage: longreadqc filterfq [options]
Options:
-h, --help output this usage information
-i, --input_file path to the input fastq file. Use this argument if only you have only one input file
-l, --input_list_file a file that contains the paths of all the input fastq files. Usage this argument if you have multiple input files
-p, --out_prefix prefix of the output file. (required)
-n, --num_split_file split the output file to n files. (not required, default: n=1)
-a, --min_read_length min read length. (not required)
-b, --max_read_length max read length. (not required)
For example,
longreadqc filterfq -i input.fastq -p ./output_prefix
longreadqc filterfq -l input.fastqs.list -p ./output_prefix -n 10
git clone https://github.com/fangli08/longreadqc.git
cd longreadqc/
make
You can copy the longreadqc binary file to the folder in your PATH.