https://github.com/robaina/filtersam

Tools to filter SAM/BAM files by percent identity and percent of matched sequence
https://github.com/robaina/filtersam

alignment bioinformatics computational-biology genomics python samtools sequence-alignment

Last synced: 3 months ago
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Tools to filter SAM/BAM files by percent identity and percent of matched sequence

• Host: GitHub
• URL: https://github.com/robaina/filtersam
• Owner: Robaina
• License: apache-2.0
• Created: 2021-08-28T18:41:26.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-06-06T08:57:54.000Z (about 2 years ago)
• Last Synced: 2025-03-10T22:37:36.622Z (4 months ago)
• Topics: alignment, bioinformatics, computational-biology, genomics, python, samtools, sequence-alignment
• Language: Python
• Homepage:
• Size: 313 KB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md
  • Citation: CITATION.cff

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README

        
![logo](assets/logo.png)

## 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](https://lh3.github.io/2018/11/25/on-the-definition-of-sequence-identity).

2. BAM/SAM files must contain [MD tags](https://github.com/vsbuffalo/devnotes/wiki/The-MD-Tag-in-BAM-Files) to be able to filter by percent identity. Aligners such as [BWA](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2705234/) add MD tags to each queried sequence in a BAM file. MD tags can also be generated with [samtools](http://www.htslib.org/doc/samtools-calmd.html).

## Installation

```pip install filtersam```

## Usage

You can find a jupyter notebook with usage examples [here](examples/examples.ipynb).

## 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.