Local Run Manager for MiniSeq Compatible Libraries

Custom Libraries

Most analysis modules prompt you to select a library prep kit when creating a run in Local Run Manager. You can create a custom library prep kit definition for use with an analysis module using tools on the Local Run Manager dashboard. See the Local Run Manager Software Guide and example kit definition files.

Supported Libraries

Amplicon Analysis Module

The Amplicon analysis module aligns reads against the reference specified in the manifest file, and then performs variant analysis.

Library Kit Category Library Kit Name
TruSeq Amplicon

TruSeq Amplicon - Cancer Panel

TruSeq Custom Amplicon 1.5

TruSeq Custom Amplicon Low Input

TruSight Amplicon Panels

TruSight Myeloid Panel

Amplicon DS Analysis Module

Designed specifically for dual-strand targeted resequencing assays, the Amplicon DS analysis module aligns reads against the reference specified in the manifest file, and then performs variant analysis.

Library Kit Category Library Kit Name

TruSeq Amplicon

TruSeq Custom Amplicon 1.5 (if Dual Strand was specified in DesignStudio)

TruSeq Custom Amplicon Low Input (if Dual Strand was specified in DesignStudio)

TruSight Amplicon Panels

TruSight Tumor 26

DNA Enrichment Analysis Module

The DNA Enrichment analysis module aligns reads against the whole genome reference, and then performs variant analysis for regions of interest specified in the manifest file.

Library Kit Category Library Kit Name

Nextera Rapid Capture Enrichment

Nextera Rapid Capture

TruSight Enrichment Panels

TruSight Rapid Capture, including:
  • TruSight Autism
  • TruSight Cancer
  • TruSight Inherited Disease
Generate FASTQ Analysis Module

The Generate FASTQ analysis module demultiplexes indexed reads, generates intermediate analysis files in the FASTQ file format, and then exits the workflow. FASTQ files are input for third-party analysis tools.

Library Kit Category Library Kit Name

TruSeq Amplicon

TruSeq Amplicon - Cancer Panel

TruSeq Custom Amplicon 1.5

TruSeq Custom Amplicon Low Input

TruSight Amplicon Panels

TruSight Myeloid Panel

Nextera

Nextera DNA

Nextera Mate Pair

Nextera Mate Pair

Nextera XT V2

Nextera XT with Index Kits v2

Nextera XT

Nextera XT

TruSeq HT

TruSeq Nano DNA HT

TruSeq DNA PCR-Free HT

TruSeq LT

TruSeq Nano DNA LT

TruSeq DNA PCR-Free LT

Nextera Rapid Capture Enrichment

Nextera Rapid Capture

TruSight Enrichment Panels

TruSight One

TruSight Rapid Capture, including:

  • TruSight Autism
  • TruSight Cancer
  • TruSight Inherited Disease

TruSeq Small RNA

TruSeq Small RNA

Resequencing Analysis Module

Intended for whole-genome sequencing of small genomes, the Resequencing analysis module aligns reads against the specified reference, and then performs variant analysis.

Library Kit Category Library Kit Name

Nextera

Nextera DNA

Nextera XT V2

Nextera XT with Index Kits v2

Nextera XT

Nextera XT

TruSeq HT

TruSeq Nano DNA HT

TruSeq DNA PCR-Free HT

TruSeq LT

TruSeq Nano DNA LT

TruSeq DNA PCR-Free LT

Small RNA Analysis Module

The Small RNA analysis module aligns reads against databases for contaminants, mature miRNA, small RNA, and a genomic reference, and then measures abundance of short RNA sequences.

By default, the analysis module is set to TruSeq Small RNA libraries.

Targeted RNA Analysis Module

The Targeted RNA analysis module aligns reads specified in the manifest file, quantifies the relative expression of genes and isoforms between samples, and then compares abundance across samples.

By default, the analysis module is set to TruSeq Targeted RNA Expression libraries.

TruSight Tumor 15 Analysis Module

The TruSight Tumor 15 analysis module aligns reads specified in the manifest file, and then reports somatic variants of a set of reference panel genes associated with cancer.

By default, the analysis module is set to TruSight Tumor 15 libraries.