Ordering the TGACv1 CS42 wheat genome assembly scaffolds using a genetic map

Data

All data is from https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0582-8

1. Marker sequences: W7984 scaffolds from Chapman et al. (2015) http://dx.doi.org/10.5447/IPK/2014/14
2. Genetic map (W7984 x Opata M85) coordinates: Supplementary Dataset S4 from Chapman et al. (2015) http://dx.doi.org/10.5447/IPK/2014/10

Correcting the W7984 x Opata M85 map

We corrected the genetic distances between bins by iterating over the bins b and merging bins bi and bi+1 into bi’ if:

• |b(i)-b(i+1)| < 1.6 recombinations (1 recombination represents 0.586 cM on the WGS map)
• b(i)’ did not span more than 2.5 cM [Abraham Korol - pers. comm.].

The map position for each b(i)’ was calculated as the arithmetic mean of all bins merged into it. This is done by the script chapman_repair.py.

Anchoring TGACv1 scaffolds on W7984 x Opata M85 map

W7984 scaffolds are aligned against TGACv1 scaffolds using megablast.

##### megablast parameters blastn -max_target_seqs 1 -evalue 1e-10 -outfmt "7 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen qseq sseq nident mismatch positive gapopen gpas ppos qcovs qcovhsp sstrand qseq sseq"

Create raw map

With map_blast.py.

Generate scaffold classifications

With classify_scaffolds.py.