Tutorial¶

This tutorial walks through a complete teloclip run, from installing the tool to validating the extended assembly.

Each stage is a separate page and builds on the previous one. The commands use a consistent set of filenames so you can follow along end to end.

Stage	Page	Produces
1	Installation	A working `teloclip` and `samtools`
2	Mapping reads	`raw.bam` and its index
3	Filtering overhangs	`overhangs.bam`
4	Extracting reads	Per-contig-end FASTA files
5	Extending contigs	`extended.fasta` and a stats report
6	Validating the result	Confidence, or a reason to stop

What you need¶

A draft assembly in FASTA format (ref.fa)
The long reads used to build it (reads.fq.gz)
minimap2 and samtools

Reads should be the raw long reads, not the corrected or trimmed set — teloclip needs the sequence the assembler discarded, which correction may remove.

Files used throughout¶

ref.fa              draft assembly
ref.fa.fai          its index
reads.fq.gz         raw long reads
raw.bam             all alignments
overhangs.bam       alignments clipped at contig ends
extended.fasta      the result
extension_report.md what changed and why

Before you start¶

Know your organism's telomeric repeat. The canonical vertebrate repeat is TTAGGG, but plants commonly use TTTAGGG, and many fungi and protists differ again. Passing the wrong motif to --motifs will silently discard the reads you want.

If you do not know it, run filter without --motifs first and inspect the clipped sequences with extract — the repeat is usually obvious once you look at them.