We performed correction of raw reads for the A. halleri ssp.
Supplementary Table 1 indicates the number of raw reads successfully aligned for each of the samples.
(b) STAR Alignment total number of raw reads compared to number of mapped reads listed per sample.
The ErrorCorrectReads.pl module of ALLPATHS-LG version 44837 was used for correction of raw reads (34.0 million reads).
An individual barcode could be assigned to about 81% of raw reads yielding ~1.3 million retained reads per sample.
All libraries had been down sampled to the same amount of raw reads prior to mapping and annotation.
In total, we generated 66.9, 64.6, 64.9 and 60.3 Gb of raw reads for linked-read sequencing (hC, hA, h, and C. septempunctata, respectively).
In total, we obtained 232.72, 93.80, 79.74 and 66.65 Gb (Supplementary Table 1) of raw reads from the libraries of BP, PM, SH and PS, respectively.
Quality control (QC), mapping, and processing of raw reads were performed as follows.
The original sequencing data of raw reads were deposited in the sequence read archive of the National Center for Biotechnology (Aaccession Nos. PRJNA294127, SRR2242800, and SRS1048835).
The original sequencing data of raw reads were deposited in the sequence read archive of the National Center for Biotechnology (accession nos. PRJNA437450, SRP134182).
