Input file types

STRmie-HD is optimized for high-quality targeted sequencing data (e.g., Illumina MiSeq, PacBio SMRT).
Its performance may be reduced on lower-coverage or noisier platforms (such as Oxford Nanopore) or in whole-genome/low-depth clinical pipelines, where additional parameter tuning or error-correction strategies may be required.

Because the tool relies on exact regular-expression matching to identify repeat tracts and interruption motifs, reads with sequencing errors or incomplete coverage of the repeat region may be excluded from the analysis.
As a result, STRmie-HD performs best when applied to datasets with high sequencing accuracy and sufficient coverage of the target locus.

STRmie-HD accepts as input:

• fastq.gz → gzipped file of raw reads with base calls and quality scores.

• fasta.gz → gzipped file of sequences without quality scores.

💡 Tip: Merging is especially useful for repeat-rich regions (e.g., HTT), where overlap-aware merging improves accuracy by using base qualities and positional evidence.