In certain workflows, you may be able to specify a Manifest file in the Reference Sequence screen.

Manifest files are tab-separated files used to define the chromosomal coordinates of gene targets in the assembly, and are normally generated automatically , e.g., by Illumina. (See Illumina’s manifest file PDF for a description.) Manifest files can have various file extensions, though .txt is commonly used.

SeqMan NGen can read and produce output using a variety of common chromosome naming conventions, including “chr1” and “ch1,” as well as Arabic and Roman numerals. Chromosome names are captured from genome template packages and used to assign contig IDs to entries from BED, VCF and manifest files.

The following examples show the most basic required columns for the manifest file, as well as two formats that are used by Illumina. These examples are provided in case you need to trouble-shoot problems with existing manifest files. If you want to create your own targeted regions file, we recommend making a BED file rather than a manifest file. See Make a custom BED file for detailed instructions.

The columns below can appear in any order. Columns with blue headers are required, while columns with orange headers are optional.

User-made file (most basic version):

Name Chromosome Start End
28324371 chrM 577 647

Illumina manifest file – format 1:

TargetA TargetB Target Number Chromosome Start Position End Position Probe Strand Sequence Species Build ID
chr1.43815008.43815009 chr1.43815008.43815009 1 chr1 43814982 43815163 + GGTGCC Homo sapiens hg19
chr1.115256528.115256531 chr1.115256528.115256531 1 chr1 115256500 115256680 + TCTTTA Homo sapiens hg19

Illumina manifest file – format 2:

Name Chromosome Start End Upstream Probe Length Downstream Probe Length
28324371 chrM 577 647 0 0

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