README.md

HTSinfer

HTSinfer infers RNA-Seq metadata from Illumina high-throughput sequencing (HTS) data.

Quick start

For a more in-depth guide please refer to the HTSinfer documentation.

Installation

HTSinfer is available on Bioconda. To install it in your currently active Conda environment, run:

conda install bioconda::htsinfer

General usage

htsinfer [-h] [--verbosity {DEBUG,INFO,WARN,ERROR,CRITICAL}] [--version]       
         PATH [PATH]

Examples

Single-ended library

htsinfer tests/files/adapter_single.fastq

Paired-ended library

htsinfer tests/files/adapter_1.fastq tests/files/adapter_2.fastq

Output is written to STDOUT in JSON format. The log is written to STDERR.

Example output

This is the output (STDOUT) of the above-mentioned call on a paired-ended example library:

{
   "library_stats": {
      "file_1": {
         "read_length": {
            "min": 75,
            "max": 75,
            "mean": 75.0,
            "median": 75,
            "mode": 75
         }
      },
      "file_2": {
         "read_length": {
            "min": 75,
            "max": 75,
            "mean": 75.0,
            "median": 75,
            "mode": 75
         }
      }
   },
   "library_source": {
      "file_1": {
         "short_name": "hsapiens",
         "taxon_id": "9606"
      },
      "file_2": {
         "short_name": "hsapiens",
         "taxon_id": "9606"
      }
   },
   "library_type": {
      "file_1": "first_mate",
      "file_2": "second_mate",
      "relationship": "split_mates"
   },
   "read_orientation": {
      "file_1": "SF",
      "file_2": "SR",
      "relationship": "ISF"
   },
   "read_layout": {
      "file_1": {
         "adapt_3": "AATGATACGGCGACC",
         "polyA_frac": 10.0
      },
      "file_2": {
         "adapt_3": "AATGATACGGCGACC",
         "polyA_frac": 10.0
      }
   }
}

To better understand the output, please refer to the Results section in the documentation.

Versioning

The project follows the Semantic Versioning guidelines for version management. Currently, the service is in its beta phase, meaning API breaking changes or updates may occur without prior notice.

Contributing

This project lives off your contributions, be it in the form of bug reports, feature requests, discussions, or fixes and other code changes. Please refer to the contributing guidelines if you are interested to contribute. Please mind the code of conduct for all interactions with the community.

Contact

For questions or suggestions regarding the code, please use the issue tracker. For any other inquiries, please contact us by email: [email protected]

(c) 2020 Zavolan lab, Biozentrum, University of Basel