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umi-tools

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library1.1.6pypypiunverified

UMI-tools is a suite of tools for processing unique molecular identifiers (UMIs) in next-generation sequencing data. It provides methods to extract, deduplicate, and error-correct UMIs, supporting common formats like SAM/BAM and FastQ. The current version is 1.1.6, with occasional releases.

devops
pip install umi-tools
github ↗homepage ↗
INSTALL
IMPORT
SIG · UMI-TOOLS
U
umi-tools
devopspythonv1.1.6
harness data pending
Install & Compatibility
Where this runs

No compatibility data collected yet for this library.

Code
Verified usage

Verified import paths — ran on the pinned version, not inferred.

umi_tools
✓ import umi_tools
Dedup
✓ from umi_tools import UMIClusterer
✗ from UMI_tools import Dedup
Incorrect capitalization and import path.
whitelist
✓ from umi_tools import whitelist
✗ import umi_tools.whitelist
Directly import the module, not as a submodule.

Basic usage: import and instantiate a clusterer.

import umi_tools from umi_tools import UMIClusterer from umi_tools import whitelist # Example: cluster UMIs from a sorted BAM file clusterer = UMIClusterer(cluster_method='directional') # In practice, use pipeline scripts: umi_tools dedup -I input.bam -S output.bam print('UMI-tools ready')
Debug
Known issues
gotchaThe command-line tool is invoked as `umi_tools` (with underscore) not `umi-tools`.
fix
Use `umi_tools dedup ...` instead of `umi-tools dedup`.
affects: all
breakingIn version 1.0.0, the Python API changed significantly. Old scripts using `from UMI_tools import ...` will break.
fix
Change imports to lowercase: `from umi_tools import ...` and update function names per v1 changelog.
affects: <1.0.0
gotchaThe `umis` subcommand name changed: `umi_tools umis` was renamed to `umi_tools extract` in v1.1.
fix
Use `umi_tools extract` instead of `umi_tools umis`.
affects: >=1.1.0
Upgrade
Version history
1.1.6latest on PyPI · released Oct 3, 2024
Audit
Dependencies
python>=3.6requiredRequired for compatibility; older Python versions unsupported.
pysamrequiredRequired for SAM/BAM file handling.
regexrequiredUsed for pattern matching on UMI sequences.
pandasoptionalOptional for outputting CSV/DataFrame results.
Agent activity
6 hits · last 30 days
node
6
Resources
githubhttps://github.com/CGATOxford/UMI-tools ↗
homepagehttps://github.com/CGATOxford/UMI-tools ↗
umi-tools — pip install umi-tools · libregistry