Glycine

This tool is designed to identify and trim full-length cDNA sequencing reads.

No Installation Required

Ready to Use After Extraction

This tool is designed for ease of use without the need for a complicated installation process. Simply extract the contents of the software package to your preferred location on your system, and it's ready to go.

How to Start:

1. Download the .tar.gz file.
2. Extract the contents to a desired location.
3. Run the glycine to start the software.

Example Usage

glycine -f sample.fq.gz -5 tso-seq -3 rtp-seq -o /path/to/output -n sample -e 0.25,0.4 -s 100,100 -u 10 -l 10

Command-line Arguments

Usage: glycine [OPTIONS] --fastq <fastq file> --tso_seq <tso seq> --rtp_seq <rtp seq> --outdir <output dir> --sample <sample>

Options:
  -f, --fastq <fastq file>       Input a fastq file
  -5, --tso_seq <tso seq>        TSO sequence
  -3, --rtp_seq <rtp seq>        RTP sequence
  -o, --outdir <output dir>      Output directory
  -n, --sample <sample>          Sample name
  -e, --err <err threshold>      Threshold of Levenshtein Distance value or sequencing error rate. Use a comma to separate two numbers, when there are
                                 different thresholds for the 5' and 3' ends [default: 0.25,0.4]
  -s, --shift <shift threshold>  Threshold of shift length for identifying TSO/RTP sequences. Use a comma to separate two numbers, when there are different
                                 thresholds for the 5' and 3' ends [default: 50,50]
  -L, --min_len <min len>        Sequences shorter than the minimum length will be directly classified as discarded [default: 100]
  -Q, --min_qual <min qual>      Read quality lower than the minimum quality will be directly classified as discarded [default: 7.0]
  -u, --trim_len <trim len>      The length of the 3' end barcode sequence to be trimmed [default: 0]
  -l, --tail_len <tail len>      PolyA tail length [default: 10]
  -q, --umi_len <umi len>        The length of the Unique Molecular Identifier (UMI) located between the PolyA tail and the Reverse Transcription Primer
                                 (RTP) [default: 0]
  -t, --thread <thread>          Number of threads [default: 4]
  -h, --help                     Print help
  -V, --version                  Print version

Versions

This tool offers two versions:
GNU version: Provides optimized performance but requires glibc version 2.35 or newer on your system.
musl version: Designed for compatibility on x86_64 Linux servers, offering a reliable alternative with slightly reduced performance compared to the glibc build.
Please choose the version that best suits your system's environment and performance needs.
The chart below compares the memory usage of two versions over time, for a 10.87 GB dataset processed using 4 threads.

Authors

夏小双 Xiaoshuang Xia ([email protected])

License and Usage Restrictions

Research Use Only

This software is provided strictly for individual research purposes. Commercial use is strictly prohibited. This means:
Allowed: Personal academic research, personal learning, and non-commercial experimentation.
Not Allowed: Any form of commercial application, distribution, or use that generates revenue directly or indirectly. This includes, but is not limited to, integration into commercial products, offering this software as a service, or using it for commercial gain.

For commercial licensing or permissions, please contact us.