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partis

Provides an Hidden Markov Model (HMM)-based framework for studying B-cell receptor sequence (BCRs). Partis is an open source software able to annotate, simulate, and infer clonal family of BCRs. The program deduces parameters about the rearrangement process before performing annotation inference on each sequence in the set. It intends to be effective for analyzing modern large sequencing data sets.

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partis classification

partis specifications

Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTA
Output format:
CSV
Programming languages:
C, C++, Perl, Python
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Input data:
B-cell receptor sequences, parameters particular to the input sequence file
Output data:
The germline genes used to make the BCR, the amount of junctional exonuclease deletion for each gene, the size of junctional insertions (N-regions) between the trimmed germline genes, the joint probability of sequence and annotation
Operating system:
Unix/Linux
License:
GNU General Public License version 3.0
Version:
0.13.0
Requirements:
ham, ig-sw

partis distribution

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partis support

Documentation

Maintainers

  • Frederick A. Matsen <>
  • Duncan Ralph <>

Credits

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Publications

Institution(s)

Fred Hutch, Seattle, Washington, USA

Funding source(s)

Supported by NIH grants U19- AI117891, R01-GM113246, and R01-AI12096 and, in part, by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation.

Link to literature

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