Protocols

MinorityReport specifications

Information


Unique identifier OMICS_14697
Name MinorityReport
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Reference sequence, gene annotation file, parent strain, child/mutant strain.
Input format FASTA, GFF, SAM
Output data All variants over n% abundant in reads mapped to this position, unique in child w.r.t. parent or statistics of read ratios for each tile.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Jeremy Horst

Publication for MinorityReport

MinorityReport citation

call_split

Plasmid free CRISPR/Cas9 genome editing in Plasmodium falciparum confirms mutations conferring resistance to the dihydroisoquinolone clinical candidate SJ733

2017
PLoS One
PMCID: 5439709
PMID: 28542423
DOI: 10.1371/journal.pone.0178163
call_split See protocol

[…] ucleotide Alignment Program) [] with the following flags: “—gmap-mode = none—batch = 4—npaths = 1—maxsearch = 10.” The resulting SAM files were imported into Geneious version 8.1.8 [] and run through MinorityReport to assess genetic differences []. Aligned sequencing reads for ACP-B6 and each mutant strain were input along with the FASTA and GFF files for the 3D7 reference genome from PlasmoDB, ve […]

MinorityReport institution(s)
Department of Biochemistry and Biophysics, University of California San Francisco School of Medicine, CA, USA; Howard Hughes Medical Institute, MD, USA
MinorityReport funding source(s)
Supported by NIH/NIDCR training grant T32-DE007306, by the Philippine California Advanced Research Institutes project IHITM 63 and by the Howard Hughes Medical Institute.

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