├── .github └── workflows │ └── ubuntu-distcheck.yml ├── .gitignore ├── .readthedocs.yaml ├── Configuration ├── adapter_list.txt ├── contaminant_list.txt └── limits.txt ├── LICENSE ├── Makefile ├── Makefile.am ├── README.md ├── autogen.sh ├── benchmark ├── README.md ├── download_files.sh ├── outs │ ├── falco │ │ ├── README.md │ │ ├── SRR10124060_rnaseq.fastq_qc_data.txt │ │ └── SRR10124060_rnaseq.fastq_report.html │ ├── fastp │ │ ├── SRR10124060_rnaseq.fastq.html │ │ └── SRR10124060_rnaseq.fastq.json │ └── fastqc │ │ ├── README.md │ │ └── SRR10124060_rnaseq_fastqc │ │ ├── fastqc_data.txt │ │ └── fastqc_report.html ├── run_all_falco_tests.sh ├── run_all_fastp_tests.sh ├── run_all_fastqc_tests.sh ├── run_all_htqc_tests.sh └── tests │ └── README.md ├── configure.ac ├── documentation ├── README.md ├── docs │ └── index.md └── mkdocs.yml ├── example.bam ├── example.fq ├── example.sam ├── m4 ├── ax_cxx_check_lib.m4 ├── ax_cxx_compile_stdcxx.m4 └── ax_cxx_compile_stdcxx_17.m4 ├── src ├── 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