README.md

lrma

Scripts and data for the analysis of transposable elements in hybrid yeast mutation accumulation (MA) lines with long reads

Main scripts

rates.ipynb

Analysis of Ty1 transposition fluctuation assays

sort_reads.ipynb

Sorting of long-read libraries into subgenomes

sv.ipynb

Classification of TE orthogroups into SV types

te_annot.ipynb

Processing of TE annotations

Subfolders description

depth/

Compute depth of coverage from sorted libraries mapped on rDNA-masked parental assemblies

depth_bins/

Binned depth of coverage data for manual visualization of polyploidy/aneuploidy/LOH loci

depth_tracts/

Depth of coverage data merged by tracts

liftover/

Conversion of subgenome assembly coordinates into parental coordinates

medaka/

Polished subgenome-level assemblies

minimap_aln/

Reciprocal alignment of subgenome assemblies and rDNA-masked parental assemblies for liftover and reverse-liftover

minimap_misassembly/ (deprecated)

Mapping of sorted libraries on subgenome assemblies

minimap_sort/

Mapping of long-read libraries for sorting

mummer_crosses/

Alignment of parental genomes for Ty loci orthology

mummer_polished/

Alignment of polished subgenome assemblies against parental assemblies

private_variants/

Extraction of genomic variants that discriminate the parents of each cross

REannotate_output/

Processing of RepeatMasker TE annotations

RepeatMasker/

TE annotation in subgenome assemblies

reverse_liftover/

Conversion of parental coordinates into subgenome assembly coordinates

script/

Main scripts

seqkit_stats/

Stats on raw basecalled read libraries

sort/

Sorting of long-read libraries into subgenomes

wtdbg2/

Assembly of subgenomes