MICADo specifications

Information


Unique identifier OMICS_27043
Name MICADo
Software type Application/Script
Interface Command line interface
Restrictions to use None
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.
Input format FASTQ+FASTA/TSV
Output format JSON,TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
Computer skills Advanced
Version 1.0
Stability Stable
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
Maintained Yes

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Documentation


Maintainers


  • person_outline Justine Rudewicz <>
  • person_outline Hayssam Soueidan <>
  • person_outline Macha Nikolski <>

Publication for MICADo

library_books

MICADo - Looking for Mutations in Targeted PacBio Cancer Data: An Alignment-Free Method.

2016 Front Genet
PMCID: 5143680
PMID: 28008336
DOI: 10.3389/fgene.2016.00214
MICADo 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
MICADo 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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