{"id":46722,"library":"umi-tools","title":"UMI-tools","description":"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.","status":"active","version":"1.1.6","language":"python","source_language":"en","source_url":"https://github.com/CGATOxford/UMI-tools","tags":["bioinformatics","UMI","sequencing","dedup"],"install":[{"cmd":"pip install umi-tools","lang":"bash","label":"PyPI"}],"dependencies":[{"reason":"Required for compatibility; older Python versions unsupported.","package":"python>=3.6","optional":false},{"reason":"Required for SAM/BAM file handling.","package":"pysam","optional":false},{"reason":"Used for pattern matching on UMI sequences.","package":"regex","optional":false},{"reason":"Optional for outputting CSV/DataFrame results.","package":"pandas","optional":true}],"imports":[{"note":"","wrong":"","symbol":"umi_tools","correct":"import umi_tools"},{"note":"Incorrect capitalization and import path.","wrong":"from UMI_tools import Dedup","symbol":"Dedup","correct":"from umi_tools import UMIClusterer"},{"note":"Directly import the module, not as a submodule.","wrong":"import umi_tools.whitelist","symbol":"whitelist","correct":"from umi_tools import whitelist"}],"quickstart":{"code":"import umi_tools\nfrom umi_tools import UMIClusterer\nfrom umi_tools import whitelist\n# Example: cluster UMIs from a sorted BAM file\nclusterer = UMIClusterer(cluster_method='directional')\n# In practice, use pipeline scripts: umi_tools dedup -I input.bam -S output.bam\nprint('UMI-tools ready')","lang":"python","description":"Basic usage: import and instantiate a clusterer."},"warnings":[{"fix":"Use `umi_tools dedup ...` instead of `umi-tools dedup`.","message":"The command-line tool is invoked as `umi_tools` (with underscore) not `umi-tools`.","severity":"gotcha","affected_versions":"all"},{"fix":"Change imports to lowercase: `from umi_tools import ...` and update function names per v1 changelog.","message":"In version 1.0.0, the Python API changed significantly. Old scripts using `from UMI_tools import ...` will break.","severity":"breaking","affected_versions":"<1.0.0"},{"fix":"Use `umi_tools extract` instead of `umi_tools umis`.","message":"The `umis` subcommand name changed: `umi_tools umis` was renamed to `umi_tools extract` in v1.1.","severity":"gotcha","affected_versions":">=1.1.0"}],"env_vars":null,"search_vec":"'1.1.6':46 'bioinformat':50 'common':36 'correct':33 'current':43 'data':23 'dedup':53 'dedupl':29 'error':32 'error-correct':31 'extract':28 'fastq':41 'format':37 'generat':21 'identifi':16 'like':38 'method':26 'molecular':15 'next':20 'next-gener':19 'occasion':48 'process':13 'provid':25 'releas':49 'sam/bam':39 'sequenc':22,52 'suit':9 'support':35 'tool':3,6,11 'umi':2,5,17,34,51 'umi-tool':1,4 'uniqu':14 'version':44","created_at":"2026-06-07T13:01:18.202748+00:00","updated_at":"2026-06-07T13:01:18.202748+00:00","problems":{"verify_error":"× Failed to build `umi-tools==1.1.6`\n  ├─▶ The build backend returned an error\n  ╰─▶ Call to `setuptools.build_meta:__legacy__.build_wheel` failed (exit\n      status: 1)\n\n      [stderr]\n      Downloading\n      https://pypi.io/packages/source/s/setuptools/setuptools-10.0.zip\n      Extracting in /tmp/"},"ecosystem":"pypi","meta_description":null,"install_score":null,"quickstart_score":null,"quickstart_tag":null,"pypi_latest":null,"cli_name":null,"cli_version":null,"type":"library","homepage":"https://github.com/CGATOxford/UMI-tools","github":"https://github.com/CGATOxford/UMI-tools","docs":null,"changelog":null,"pypi":null,"npm":null,"openapi_spec":null,"status_page":null,"smithery":null,"categories":["devops"],"base_url":null,"auth_type":null,"provenance":{"verified_status":"install_fail","verified_at":"2026-06-29","last_verified":"2026-06-29","next_check":"2026-07-06","install_tag":null}}