seq-miner

seq-miner is a lightweight tool to extract and filter reads from BAM or FASTQ files based on:

Specific read IDs
Mean quality score threshold
Minimum read length
Multi-threading (FASTQ)
JSON/CSV-ready summary (optional)

Installation

pip install seq-miner

Or clone from source:

git clone https://github.com/your-org/seq-miner.git
cd seq-miner
pip install .

Usage

Extract reads from BAM

seq-miner -i reads.bam -o filtered.bam -f bam -r read_ids.txt --min-qscore 10 --min-length 200

Filter FASTQ reads in parallel

seq-miner -i reads.fastq -o filtered.fastq -f fastq --min-qscore 15 --min-length 1000 --threads 4

Show version

seq-miner --version

Command-line Options

Option	Description
`-i`, `--input`	Input BAM or FASTQ file
`-o`, `--output`	Output file for passed reads
`-f`, `--format`	File format: `bam` or `fastq`
`-r`, `--read-ids`	Optional file with read IDs (one per line)
`--min-qscore`	Minimum mean Q-score (default: `0.0`)
`--min-length`	Minimum read length (default: `0`)
`--threads`	Number of CPU threads (only used for FASTQ)
`--verbose`	Enable verbose logging
`--version`	Print the current version

Output Summary

When finished, you'll see:

Summary:
Passed reads     : 12345
Low-quality reads : 54
Short reads      : 91

Optionally, you can pipe this to JSON or CSV (coming soon).

Auto Version + Release

Version is stored in seqminer/__version__.py
Tagged automatically with GitHub Actions on push to main
Published to PyPI on GitHub release

License

MIT License © Theerayut
See LICENSE for full text.

Contact

For issues, please open an issue on GitHub.

Metadata

Release files for seq-miner 1.3.1

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Source distribution (sdist)

Source distribution for seq-miner 1.3.1
File	Size	Uploaded	Provenance
seq_miner-1.3.1.tar.gz	5.7 kB	Jul 22, 2025	With provenance	Details

Built distribution (wheel)

Table of built distributions (wheels) for seq-miner 1.3.1
File	Interpreter	ABI	Platform	Reset
seq_miner-1.3.1-py3-none-any.whl 6.4 kB Jul 22, 2025 With provenance	Python 3	none	any	Details

Total release size: 12.1 kB

Release files / seq_miner-1.3.1.tar.gz

Download URL	seq_miner-1.3.1.tar.gz
Size	5.7 kB
Tags	Source
SHA-256 checksum How to use checksums	`8ef78d9b0748bea2889d15cf34c5e437be9ad67d04a69326cb5d2819e02a9cf1`
BLAKE2b-256 checksum How to use checksums	`cdf401d17a59f67722034da4a78d3df96c47170f6a649b7cecd46d4c08fa3413`
Upload date	Jul 22, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

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Publishing platform: GitHub Actions
Publishing repository: github.com/aeiwz/seq-miner
Publishing commit: github.com/aeiwz/seq-miner/tree/d97c05c36c0f999a9bfcbd4afae6628f536b0199

Workflow

Publishing configuration: github.com/aeiwz/seq-miner/blob/d97c05c36c0f999a9bfcbd4afae6628f536b0199/.github/workflows/python-publish.yml
Publishing logs: github.com/aeiwz/seq-miner/actions/runs/16434196166/attempts/1

Artifact

Subject: seq_miner-1.3.1.tar.gz
SHA-256 checksum: 8ef78d9b0748bea2889d15cf34c5e437be9ad67d04a69326cb5d2819e02a9cf1 Verifying attestations

Release files / seq_miner-1.3.1-py3-none-any.whl

Download URL	seq_miner-1.3.1-py3-none-any.whl
Size	6.4 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`4d8ef02596427e4b013dedac2c4eafbe292d24ae9f0440e25abe8b0e053090bc`
BLAKE2b-256 checksum How to use checksums	`d1c4c564e4aa87b6afc025c35b58b12b71be73da34e106523ddfde48c6b45ff1`
Upload date	Jul 22, 2025
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.12.9`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/aeiwz/seq-miner
Publishing commit: github.com/aeiwz/seq-miner/tree/d97c05c36c0f999a9bfcbd4afae6628f536b0199

Workflow

Publishing configuration: github.com/aeiwz/seq-miner/blob/d97c05c36c0f999a9bfcbd4afae6628f536b0199/.github/workflows/python-publish.yml
Publishing logs: github.com/aeiwz/seq-miner/actions/runs/16434196166/attempts/1

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Subject: seq_miner-1.3.1-py3-none-any.whl
SHA-256 checksum: 4d8ef02596427e4b013dedac2c4eafbe292d24ae9f0440e25abe8b0e053090bc Verifying attestations

Security for seq-miner 1.3.1

Report project as malware

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Attestation for seq_miner-1.3.1.tar.gz

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/aeiwz/seq-miner
Publishing commit: github.com/aeiwz/seq-miner/tree/d97c05c36c0f999a9bfcbd4afae6628f536b0199

Workflow

Publishing configuration: github.com/aeiwz/seq-miner/blob/d97c05c36c0f999a9bfcbd4afae6628f536b0199/.github/workflows/python-publish.yml
Publishing logs: github.com/aeiwz/seq-miner/actions/runs/16434196166/attempts/1

Artifact

Subject: seq_miner-1.3.1.tar.gz
SHA-256 checksum: 8ef78d9b0748bea2889d15cf34c5e437be9ad67d04a69326cb5d2819e02a9cf1 Verifying attestations

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