Sample Sheet Settings for Analysis
MiSeq Sample Sheet Quick Reference Guide
15
Parameter Description
ReverseComplement For the Assembly workflow, Library QC workflow,
and Resequencing workflow
Settings are 0 or 1. Default is 1, reads are reverse-
complemented.
If set to true (1), all reads are reverse-complemented as
they are written to FASTQfiles. This setting is necessary
in certain cases, such as processing of mate pair data
using BWA, which expects paired-end data. Per-cycle
metrics might be disrupted by this setting.
Set this setting to 1 when using the Resequencing
workflow or Assembly workflow with Nextera Mate
Pair libraries.
Set this setting to 1 when using the Workflow workflow
with Nextera Mate Pair libraries.
StitchReads For the Amplicon - DS workflow, Generate FASTQ
workflow, and TruSeq Amplicon workflow
Settings are 0 or 1. Default is 0, paired-end reads are not
stitched.
If set to true (1), paired end reads that overlap are
stitched to form a single read. To be stitched, a minimum
of 10 bases must overlap between Read 1 and Read 2.
Paired-end reads that cannot be stitched are converted
to two single reads.
This setting requires MiSeq Reporter v2.3.
For more information, see Read Stitching on page 17.
TaxonomyFile For the Metagenomics workflow
This setting overrides the taxonomy database; default is
taxonomy.dat.
As of MiSeq Reporter v2.3, species-level classification is
enabled, by default. For faster, but less granular genus-
level classification, specify gg_13_5_genus_32bp.dat.
VariantCaller For the Enrichment workflow, PCRAmplicon
workflow, Resequencing workflow, and TruSeq
Amplicon workflow
Specify one of the following variant caller settings:
• GATK (default)
• Somatic (recommended for tumor samples)
• Starling (legacy variant caller)
• None (no variant calling)
When using the default variant caller for the workflow,
it is not necessary to specify the variant calling method
in the sample sheet.
Adapter Settings
Some clusters can sequence beyond the sample DNA and read bases from a sequencing
adapter, particularly with longer read lengths up to 250 cycles.
The Adapter sample sheet setting prevents reporting sequence beyond the sample DNA
by trimming the specified sequence in FASTQ files. Trimming the adapter sequence
avoids reporting of spurious mismatches with the reference sequence, and improves
performance in accuracy and speed of alignment.