Comparison of MiSeq Reporter and Local Run Manager analysis workflows
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The sequencing system has had several iteration of control software and onboard analysis options. Older systems running Windows 7 have either MiSeq Control Software (MCS) 2 with MiSeq Reporter or MCS 3.1 with Local Run Manager (LRM) 2. Updating the system to Windows 10 initially included MCS version 4.0 and LRM version 3, which has now been updated to MCS version 4.1 and LRM version 4. During the system updates, older software such as MiSeq Reporter or earlier versions of LRM are replaced on the instrument by the latest version of LRM. LRM is used for both run setup and secondary analysis.
LRM secondary analysis workflows are installed as separate modules, providing the flexibility of only installing needed pipelines.
This article provides information comparing the on-instrument analysis options available for each MiSeq system version for users updating to the latest LRM version.
Neither older and non-instrument versions of MiSeq Reporter or LRM may not be co-installed on a MiSeq instrument.
A is available to make sure that the correct module version is installed for each framework version.
Analysis Workflow
MiSeq Reporter workflow
(MCS 2.6 and lower)
LRM v2 module
(MCS v3.1)
LRM v3 module
(MCS v4.0)
LRM v4 module
(MCS v4.1)
FASTQ Generation
Generate FASTQ
Generate FASTQ v2.0 or v2.1.0.28
Generate FASTQ v3.0.0.14 or v3.1.0.35
Generate FASTQ v3.0.1.1 or v3.1.0.35
Library QC
Library QC
Library QC v1.0 and v1.1
Library QC v2.1.0.18
Library QC v2.1.0.18
Small genome sequencing
Resequencing
Resequencing v2.0
Resequencing v3.0.1.13
Resequencing v3.0.1.13
DNA Enrichment
Enrichment
DNA Enrichment v2.0
DNA Enrichment v3.0.0.23
DNA Enrichment v3.0.0.23
AmpliSeq (DNA)
N/A
DNA Amplicon v2.1
DNA Amplicon v3.0.0.14
DNA Amplicon v3.0.1.1
TruSeq Amplicon
TruSeq Amplicon
DNA Amplicon v2.1
DNA Amplicon v3.0.0.14
DNA Amplicon v3.0.1.1
16S Metagenomics
Metagenomics
16s Metagenomics v1.0
16s Metagenomics v2.0.0.5
16s Metagenomics v2.0.0.5
AmpliSeq (RNA)
N/A
RNA Amplicon v2.0
RNA Amplicon v3.0.0.26
RNA Amplicon v3.0.0.26
Targeted RNA Expression
Targeted RNA
RNA Amplicon v2.0
RNA Amplicon v3.0.0.26
RNA Amplicon v3.0.0.26
TruSight Tumor 15
TruSight Tumor 15
TruSight Tumor 15 v2.0
N/A
TBD
PCR Amplicon
PCR Amplicon
PCR Amplicon v1.0
PCR Amplicon v2.0.0.26
PCR Amplicon v2.0.1.2
RNA Fusion
N/A
RNA Fusion v2.0
N/A
RNA Fusion v3.0.0.25
De novo assembly
Assembly
Assembly v1.0
Assembly v2.0.0.26
Assembly v2.0.1.2
Small RNA
Small RNA
Small RNA v2.0
N/A
Small RNA v3.0.0.24
Amplicon DS
Amplicon DS
Amplicon DS v2.0
N/A
Amplicon DS v3.0.0.56
VeriSeq PGS
VeriSeq PGS
VeriSeq PGS v1.0
N/A*
N/A*
\*VeriSeq PGS is now supported by .
For any feedback or questions regarding this article (Illumina Knowledge Article #5974), contact Illumina Technical Support .