Comparison of MiSeq Reporter and Local Run Manager analysis workflows

The MiSeq 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 LRM module selector tool 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

Small genome sequencing

Resequencing

Resequencing v2.0

Resequencing v3.0.1.13

DNA Enrichment

Enrichment

DNA Enrichment v2.0

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

AmpliSeq (RNA)

N/A

RNA Amplicon v2.0

RNA Amplicon v3.0.0.26

Targeted RNA Expression

Targeted RNA

RNA Amplicon v2.0

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*

\*VeriSeq PGS is now supported by Vitrolife.

For any feedback or questions regarding this article (Illumina Knowledge Article #5974), contact Illumina Technical Support techsupport@illumina.com.

Last updated 7 months ago