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@@ -26,11 +26,11 @@ Follow [`INSTALL.txt`](INSTALL.txt) to compile and install MashMap.
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## Parameters
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For most of the use cases, default values should be appropriate. However, different parameters and their purpose can be checked using the help page `mashmap -h`. Some of the important ones are mentioned below:
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For most of the use cases, default values should be appropriate. However, different parameters and their purpose can be checked using the help page `mashmap -h`. Important ones are mentioned below:
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* Identity threshold (--perc_identity, --pi) : By default, its set to 85, implying read mappings with 85% identity should be reported. It can be set to 80% to account for more noisy read datasets.
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* Minimum read length (-m, --minReadLen) : Defult is 5,000 bp. This is set to 5K as the current average read lengths for both ONT and PacBio are >10K. Reads below this length are ignored.
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* Minimum read length (-m, --minReadLen) : Default is 5,000 bp. This is set to 5K as the current average read lengths for both ONT and PacBio are >10K. Reads below this length are ignored.
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* Protein sequences (-a, --protein) : Use this parameter when mapping protein sequences. MashMap adjusts alphabet and k-mer size accordingly.
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