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