MICADo specifications

Unique identifier:
OMICS_27043
Interface:
Command line interface
Input data:
The reference sequences for a gene of interest and several read sets corresponding to the gene panel sequencing of a cohort of patients.
Output format:
JSON,TSV
Programming languages:
Python
Version:
1.0
Requirements:
scipy, appnope, biopython, decorator, gnureadline, ipython, ipython-genutils, msgpack-python, networkx, numexpr, numpy, pandas, path.py, pexpect, pickleshare, ptyprocess, pyparsing, python-dateutil, pytz, simplegeneric, six, traitlets, wsgiref, simplejson, python-Levenshtein, sklearn
Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTQ+FASTA/TSV
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

versioning

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MICADo distribution

download

MICADo support

Documentation

Maintainers

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Publications

Institution(s)

Centre de BioInformatique de Bordeaux, University of Bordeaux, Bordeaux, France; Laboratoire Bordelais de Recherche en Informatique, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux, France; Bergonié Cancer Institute, Institut National de la Santé et de la Recherche Médicale U1218, University of Bordeaux, Bordeaux, France; Karolinska Institute and University Hospital, Stockholm, Sweden

Funding source(s)

Supported in part by the SIRIC BRIO; by grants from the Swedish Cancer Society, Knut and Alice Wallenberg’s fund, the research funds at Radiumhemmet, Karolinska Institutet and Stockholm County Council, BRECT and ALF.

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