('Tools to filter sam o bam files by percent identity or percent of matched sequence',)
Project description
A Python tool to filter sam/bam files by percent identity or percent of matched sequence
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.
NOTE
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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