Conbase specifications

Information


Unique identifier OMICS_27867
Name Conbase
Alternative name CONfirming the allelic origin of BASEs
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A single cell and bulk files, a human reference genome and gSNV coordinates to be used for phasing.
Input format BAM+FASTA
Output data An interactive graphical file, in which genotypes in sSNV loci are color coded based on observations associated with confidence in predicted genotypes, including phased and total read depth support and presence or absence of ADO and a complementary file summarizing genotype statistic.
Output format HTML
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements
pysam
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jonas Frisen

Publication for CONfirming the allelic origin of BASEs

Conbase institution(s)
Department of Cell and Molecular Biology, Karolinska Institutet, Solna, Sweden; Department of Cell and Molecular Biology, National Bioinformatics Infrastructure, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Scilifelab, Division of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden; Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
Conbase funding source(s)
Supported by the Swedish Research Council, the Swedish Cancer Society, the Swedish Society for Strategic Research, Tobias Stiftelsen, AFA Försäkringar, the Strategic Research Programme in Stem Cells and Regenerative Medicine at Karolinska Institutet (StratRegen), Torsten Söderbergs Stiftelse and the Swedish Genomes Program (Science for Life Laboratory), and the Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab.

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