Create Galaxy Workshop for telomere characterisation and extension

[Adamtaranto]

Write a Galaxy Workshop that covers basic manual checks and telomere extension. Pending #36

See Galaxy workshop tutorial

Assess starting asm and identify motifs from raw data

• De novo telomere motif identification in asm
• Motif identification from long reads
• Motif identification from short reads
• Motif length estimation from reads
• Annotate existing telomeres, list contigs with telomeres

Check for conflicting telomere signals

• Check for internal telomeric motifs (in asm)
• Check for evidence of alternative telomere attachment point (internal soft clip reads with telo motif in clip OR contig ends with mix of overhanging reads with and without motif)

Identify contigs that should be excluded from extension

• Identify circular contigs (plasmids, mito, chloroplasts etc)
• Identify high copy contigs
• Plot overhang count vs median overhang length
• Plot overhang count vs variance of overhang length

Extend, polish, report

• Run extension module and report on telomere gain
• Map reads to full asm. Polish only extended sections.