v1.0

Finishing touches on telometer's first draft.

Added:

• better handling of "gaps" in telomere sequence which are caused by sharp drops in basecalling quality (only relevant when using HAC basecalling). There should now be no discordance between telomere measurements from HAC or SUP basecalled reads as of dorado 0.72
• batch processing of input bam files so that a maximum of 8GB of memory is needed to run telometer, making it more friendly for running on local machines. This should improve performance when measuring telomeres from high-coverage WGS data.

v0.95

Made many improvements to source code

1. Improved handling of rare telomeres with non-exact matches to canonical telomere sequence within bona fide telomere sequence. Previous versions did not count these gaps as telomere, current version does.

2. Improved sub/telomere boundary identification by incorporating a scanning window which calculates the telomere density along the read and ensures that sub/telomere boundaries are not prematurely called when there is a "gap" consisting of 1 basepair mismatched telomeric sequence at the subtelomeric boundary. The maximum tolerated gap can be altered by the user with the -g flag (default 100 bp).

3. Deprecated support for R9, only recommend R10 sequencing for telomere measurement from now on as this is the chemistry ONT will continue to support and produces better data anyhow.

4. Relatedly, common telomere miscalling errors identified from R9 chemistry reads are no longer counted as telomeric motifs, only TTAGGG and CCCTAA are (+/- 1 basepair mismatch)

v0.75

Latest release includes:

• updated benchtop protocol
• Telometer is now faster
• Telometer now additionally reports a measurement of the telomere variant region at the subtelomere boundary for each telomere read
• Added minimal test dataset and stong_subtels.fa

v0.5

sequencing

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