Cycads is a tool for quality control & error profile analysis of long-read sequencing data.
git clone --depth 1 https://github.com/QYanwei/Cycads.git
conda env create --file Cycads/environment.yml --name cycads_env
conda activate cycads_env
cd Cycads && pip install .
cycads --help
The example below generates HTML report from test/ecoli.fq.gz:
cycads --fastq test/ecoli.fq.gz --output_dir test --sample_name fastq_output
-
FASTQ quality control
cycads --fastq test/ecoli.fq.gz --output_dir test --sample_name fastq_output -
FASTQ filtering
Should set the custom filtering parameter value by users
cycads --fastq test/ecoli.fq.gz --filter --output_dir test --sample_name fastq_output -
FASTQ quality control and alignment-based error analysis
cycads --fastq test/ecoli.fq.gz --reference test/ecoli.reference.fasta --output_dir test --sample_name alignment_output -
Alignment-based error analysis based on a pre-existing BAM file
cycads --bam test/test.bam --output_dir test --sample_name bam_output
=== Cycads 0.4.0 ===
============================================================================
Quality control & Data filtering & Error analysis
for Long-read sequencing
============================================================================
usage: cycads [-h] [-f FASTQ_PATH] [-b BAM_PATH] [-r REFERENCE_PATH] [-o OUTPUT_DIR] [-n SAMPLE_NAME] [-p PLATFORM] [-s N] [--seed SEED] [-T N] [-F] [-e N]
[-Q MIN_BASE_QUALITY] [--min_length MIN_READ_LENGTH] [--max_length MAX_READ_LENGTH] [--trim_5_end N] [--trim_3_end N] [-d TARGET_DEPTH]
[-g GENOME_SIZE] [--min_homopolymer_size MIN_HOMOPOLYMER_SIZE] [--max_homopolymer_size MAX_HOMOPOLYMER_SIZE]
[--max_homopolymer_indel_size MAX_HOMOPOLYMER_INDEL_SIZE] [--alignment_threads THREADS] [--sort_threads THREADS] [--minimap2_arguments ARGUMENTS]
[--minimap2 MINIMAP2] [--samtools SAMTOOLS] [--pyfastx PYFASTX]
A tool for quality control & error profile analysis of long-read sequencing data
options:
-h, --help show this help message and exit
I/O:
Input/output arguments.
-f FASTQ_PATH, --fastq FASTQ_PATH
Input FASTQ file. Supported extensions include *.fastq and *.fastq.gz. (default: None)
-b BAM_PATH, --bam BAM_PATH
Input BAM file. (default: None)
-r REFERENCE_PATH, --reference REFERENCE_PATH
Reference FASTA file. (default: None)
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
Output direcotry. (default: cycads_output)
-n SAMPLE_NAME, --sample_name SAMPLE_NAME
Sample name displayed in output reports. (default: sample)
-p PLATFORM, --platform PLATFORM
Design for CycloneSEQ data, also adopt to ONT and PB data. (default: cyclone)
FASTQ:
Arguments for FASTQ analyses. Only effective when FASTQ_PATH is supplied.
-s N, --sample N Only include a random sample of N reads from the input FASTQ file to accelerate evaluation. (default: 10000)
--seed SEED Random seed for sampling. (default: 1)
-T N, --check_terminal_bases N
Analyze N bases at both ends of each read. (default: 200)
Filtering:
Arguments for filtering the input FASTQ file. Only effective when FASTQ_PATH is supplied.
-F, --filter Output filtered FASTQ file. Analyses are always based on the input FASTQ file. (default: False)
-e N, --extract N Randomly extract N reads from the input FASTQ file. (default: None)
-Q MIN_BASE_QUALITY, --min_base_quality MIN_BASE_QUALITY
Remove reads with mean base quality less than MIN_BASE_QUALITY. (default: 7)
--min_length MIN_READ_LENGTH
Remove reads shorter than MIN_READ_LENGTH. (default: 1)
--max_length MAX_READ_LENGTH
Remove reads longer than MAX_READ_LENGTH. (default: 1000000000)
--trim_5_end N Trim N bases from the 5' end of each read. (default: 0)
--trim_3_end N Trim N bases from the 3' end of each read. (default: 0)
-d TARGET_DEPTH, --target_depth TARGET_DEPTH
Downsample FASTQ file to TARGET_DEPTH. Requires GENOME_SIZE to be supplied. (default: None)
-g GENOME_SIZE, --genome_size GENOME_SIZE
Genome size of sequenced sample. Required if TARGET_DEPTH is set. (default: None)
Homopolymers:
Arguments related to homopolymer analyses.
--min_homopolymer_size MIN_HOMOPOLYMER_SIZE
Do not analyze homopolymers shorter than MIN_HOMOPOLYMER_SIZE. (default: 2)
--max_homopolymer_size MAX_HOMOPOLYMER_SIZE
Do not analyze homopolymers longer than MAX_HOMOPOLYMER_SIZE. (default: 9)
--max_homopolymer_indel_size MAX_HOMOPOLYMER_INDEL_SIZE
Analyze homopolymer expansion/contraction up to MAX_HOMOPOLYMER_INDEL_SIZE. (default: 4)
Alignment:
Arguments for read alignment. Only effective when FASTQ_PATH and REFERENCE_PATH are supplied.
--alignment_threads THREADS
Number of threads used in read alignment. (default: 4)
--sort_threads THREADS
Number of threads used in sorting aligned segments. (default: 1)
--minimap2_arguments ARGUMENTS
Alignment arguments to be passed to minimap2. (default: -ax map-ont --secondary=no --MD --eqx -I 10G)
Dependencies:
Arguments for custom paths to external binary dependencies. Cycads searches for binary dependencies in the following order: 1. arguments specified here; 2.
the `dependencies` folder in Cycads installation path; 3. the system $PATH environmental variable.
--minimap2 MINIMAP2 Path to Minimap2. (default: None)
--samtools SAMTOOLS Path to samtools. (default: None)
--pyfastx PYFASTX Path to pyfastx. (default: None)
Result folder example:
.
├── aligned_reads.bam
├── aligned_reads.bam.bai
├── bam.pickle
├── fastq_summary.txt
├── fq.pickle
├── HTML_report
│ ├── query_all_error_item.barplot.png
│ ├── query_all_substitution_errors.barplot.png
│ ├── query_deletion_frequency.barplot.png
│ ├── query_events_curve_idy.displot.png
│ ├── query_homopolymer_length_event.lineplot.png
│ ├── query_insertion_frequency.barplot.png
│ ├── read_gc_histplot.barplot.png
│ ├── read_head_base_content.lineplot.png
│ ├── read_head_base_quality.lineplot.png
│ ├── read_homopolymer_frequency.lineplot.png
│ ├── read_length_biostat.barplot.png
│ ├── read_length_cumulative.barplot.png
│ ├── read_length_histplot_nolog.barplot.png
│ ├── read_length_quality_cross.scatterplot.png
│ ├── read_quality_histplot.barplot.png
│ ├── read_relative_position_avg_qual.lineplot.png
│ ├── read_tail_base_content.lineplot.png
│ ├── read_tail_base_quality.lineplot.png
│ └── summary.html
├── input.symlink.fastq.gz -> /path/to/test/ecoli.fq.gz
└── input.symlink.fastq.gz.fxi
1 directory, 26 files
Please donwload the HTML_report folder and open the summary.html to check the result with Web Browser, such as Google Chrome and so on.
- Sequencing summary
- Mapping summary
