RM-seq specifications


Unique identifier OMICS_27111
Name RM-seq
Alternative name Resistance Mutation SEQuencing
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data The raw reads.
Output data A table of all annotated substitutions, insertions and deletions identified in the selected population given the original sequence.
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.0.51
Stability Beta
EMBOSS, clustal-omega, bwa, samtools, bedtools, pear, cd-hit, trimmomatic
Maintained Yes




No version available


  • person_outline Benjamin Howden
  • person_outline Timothy Stinear

Publication for Resistance Mutation SEQuencing

RM-seq citations


Adherence to antiretroviral therapy and factors affecting low medication adherence among incident HIV infected individuals during 2009–2016: A nationwide study

Sci Rep
PMCID: 5816616
PMID: 29453393
DOI: 10.1038/s41598-018-21081-x

[…] In the high adherence group, means numbers of clinic visit for follow-up tests (HIV RNA quantification test, T cell subset analysis, HIV drug resistance mutation sequencing) or ART prescription were larger, and ART prescription days per visit was longer (p < 0.0001) (Table ). The number of concomitant medication except ART was not different […]


Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency

PMCID: 3197063
PMID: 21712796
DOI: 10.3791/2953

[…] mutagen-resistant variant emerges an its emergence coincides with a return to virus titers no different from untreated controls. At this stage, a large percentage of the virus population presents the resistance mutation. Sequencing of this virus population reveals the amino acid change(s) responsible. Once identified, and isolated or newly generated, the mutagen-resistant virus may be less sensiti […]

RM-seq institution(s)
Department of Microbiology and Immunology, The University of Melbourne at the Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC, Australia; Melbourne Bioinformatics, The University of Melbourne, VIC, Australia; Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, VIC, Australia; Infection and Immunity Theme, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia
RM-seq funding source(s)
Supported by the National Health and Medical Research Council (NHMRC), Australia project grant (GNT1066791) and Research Fellowship (GNT1008549) and Practitioner Fellowship (GNT1105905).

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