10/19/21
An update for the MiSeq sequencing system is now available that includes Windows 10 and MiSeq Control Software (MCS) version 4. During the system update, MiSeq Reporter or Local Run Manager (LRM) version 2 is replaced on the instrument by LRM version 3. 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 bulletin provides information comparing the on-instrument analysis options available for each MiSeq system version for users updating to LRM version 3.
Off-instrument versions of both MiSeq Reporter and LRM version 2 and 3 are available for installation on separate Windows PCs. Neither software may be co-installed on a MiSeq instrument with MCS version 4 and LRM version 3.
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 v2.6 and lower) |
LRM v2 module (MCS v3) |
LRM v3 module (MCS v4) |
|---|---|---|---|
| FASTQ Generation | Generate FASTQ | Generate FASTQ 2.0 | Generate FASTQ 3.0 |
| Library QC | Library QC | Library QC 1.1 | Library QC 2.1 |
| Small genome sequencing | Resequencing | Resequencing 2.0 | Resequencing 3.0 |
| DNA Enrichment | Enrichment | DNA Enrichment 2.0 | DNA Enrichment 3.0 |
| AmpliSeq (DNA) | Not applicable | DNA Amplicon 2.1 | DNA Amplicon 3.0 |
| TruSeq Amplicon | TruSeq Amplicon | DNA Amplicon 2.1 | DNA Amplicon 3.0 |
| 16S Metagenomics | Metagenomics | 16S Metagenomics 1.0 | 16S Metagenomics 2.0 |
| AmpliSeq (RNA) | Not applicable | RNA Amplicon 2.0 | RNA Amplicon 3.0 |
| Targeted RNA Expression | Targeted RNA | RNA Amplicon 2.0 | RNA Amplicon 3.0 |
| PCR Amplicon | PCR Amplicon | PCR Amplicon 1.0 | PCR Amplicon 2.0a |
| RNA Fusion | Not applicable | RNA Fusion 2.0 | RNA Fusion 3.0a |
| De novo assembly | Assembly | Assembly 1.0 | Assembly 2.0b |
| Small RNA | Small RNA | Small RNA 2.0 | Small RNA 3.0b |
| Amplicon DS | Amplicon DS | Amplicon DS 2.0 | Amplicon DS 3.0b |
| TruSight Tumor 15 | TruSight Tumor 15 | TruSight Tumor 15 2.0 | TruSight Tumor 15 3.0c |
| VeriSeq PGS | VeriSeq PGS | VeriSeq PGS 1.0 | Not applicabled |
aAvailable Q4 2021
bAvailable Q1 2022
cTBD
dVeriSeq PGS is now supported by Vitrolife