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A Python tool to filter sam/bam files by percent identity or percent of matched sequence

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Percent identity is computed as:

$$PI = 100 \frac{N_m}{N_m + N_i}$$

where $N_m$ is the number of matches and $N_i$ is the number of mismatches.

Percent of matched sequences is computed as:

$$PM = 100 \frac{N_m}{L}$$

where $L$ corresponds to query sequence length.

NOTES

  1. Percent of matched sequence is also an alternative definition of percent identity used in some cases, for intance, in BLAST.

  2. BAM/SAM files must contain MD tags to be able to filter by percent identity. Aligners such as BWA add MD tags to each queried sequence in a BAM file. MD tags can also be generated with samtools.

Installation

pip install filtersam

Usage

You can find a jupyter notebook with usage examples here.

Citation

If you use this software, please cite it as below:

Robaina-Estévez, S. (2022). filterSAM: filter sam/bam files by percent identity or percent of matched sequence (Version 0.0.11)[Computer software]. https://doi.org/10.5281/zenodo.7056278.

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Credits

Author: Semidán Robaina Estévez, 2021-2022

Maintainer: Semidán Robaina Estévez

License

Creative Commons Attribution 4.0 International

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