unrecognized arguments: -j (v. 1.0.10)

[gazollavolpiano]

Hello,

Thank you very much for StrainScan development.

I am trying to use it with PE reads, but the option -j is not recognized.

The output from strainscan -h does not list -j:

usage: StrainScan.py [-h] -i INPUT_FQ -d DB_DIR [-o OUT_DIR] [-k KSIZE]
                     [-l LDEP] [-s MSN]

StrainScan - A kmer-based strain-level identification tool.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT_FQ, --input_fastq INPUT_FQ
                        The dir of input fastq data --- Required
  -d DB_DIR, --database_dir DB_DIR
                        The dir of your database --- Required
  -o OUT_DIR, --output_dir OUT_DIR
                        Output dir (default: current dir/StrainVote_Result)
  -k KSIZE, --kmer_size KSIZE
                        The size of kmer, should be odd number. (default:
                        k=31)
  -l LDEP, --low_dep LDEP
                        This parameter can be set to "1" if the sequencing
                        depth of input data is very low (e.g. < 10x). For
                        super low depth ( < 1x ), you can use "-l 2" (default:
                        -l 0)
  -s MSN, --minimum_snv_num MSN
                        The minimum number of SNV at Layer-2 identification.
                        (default: k=40)

My version is 1.0.10.

If possible, can you also explain what kind of modifications changing --low_dep does? :)

[liaoherui]

Hi, thanks for using StrainScan!

If you install StrainScan through Bioconda, then you can run the command below to use the latest GitHub version, which has more new features, including parameter "-j".

git clone https://github.com/liaoherui/StrainScan.git cd StrainScan chmod 755 library/jellyfish-linux chmod 755 library/dashing_s128 python StrainScan.py -h

The parameter --low_dep will influence some filtering cutoff of the k-mer tree. Thus, we recommend using this parameter if the depth of your input data is low, in case the program misses those low-depth strains. In addition, you can also consider using the -b parameter if you have low-depth samples, which will calculate a probability for the potential strains/clusters in the low-depth sample. If you use -b, then you don't need to consider the parameter --low_dep anymore.

Any other issues, feel free to ask! :)