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We removed a variety of reads with characteristics that could interfere with assembly prior to further analyses.
Quality filtering removed ca. 13 % of reads and duplicate filtering removed a further 35%% of reads.
Although we removed a substantial number of reads prior to assembly, both long SSR regions and retroelements were prevalent in our data and could have contributed to difficulty with assembly.
After removing adaptors, poly A reads and reads of less than 18 nt, clean reads varied from 18 million to 25 million, which occupied on average 97.81% in total reads of the six libraries, were collected.
After 5' and 3' adaptors, contamination formed by adaptor-adaptor ligation and low quality tags were removed, a total of 12.14 million reads with high quality were obtained.
We also removed all reads with a "MAPQ" alignment score < 25.
Finally, we removed any reads with a mononucleotide run greater than 24 bases.
A final check removed any reads missing their paired-end sequencing mate.
