classification.md

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Chromosome classification

This page applies to FASTA mode. GFA mode annotates graph segments but does not emit scaffold classes.

Teloscope classifies each sequence from scaffold-terminal telomere blocks only. A block counts as scaffold-terminal when it falls within -t/--terminal-limit of the sequence start or end.

Output classes

Type	Gapped variant	Meaning
t2t	gapped_t2t	one p block at the left end and one q block at the right end
incomplete	gapped_incomplete	only one terminal arm is present
misassembly	gapped_misassembly	terminal arms exist but the arrangement is wrong, or the same arm appears twice
discordant	gapped_discordant	a terminal block is present but its strand composition contradicts its position
none	gapped_none	no scaffold-terminal telomere block was detected

The gapped_ prefix is added when the sequence contains assembly gaps.

Decision order

Teloscope applies the rules in this order:

1. No scaffold-terminal blocks: none
2. Any longest terminal arm with the wrong positional orientation: discordant
3. One p block left of one q block: t2t
4. Both arms present but reversed: misassembly
5. One arm present, plus a second scaffold-terminal block of the same arm: misassembly
6. One terminal arm only: incomplete

Block labels

Each terminal block is labeled from strand balance:

• p: forward-strand dominant
• q: reverse-strand dominant
• b: balanced or mixed

The granular column in *_report.tsv shows the block pattern for each sequence.

Examples:

• PQ: one dominant p block and one dominant q block
• P: one dominant p block only
• Pq: one large p block and one smaller q block
• P*: a p block in a discordant position

Uppercase marks the longest block for that arm. * marks positional discordance.