Dear all,
I am a newbie in de novo assembly. I just used software minia 1.4683 to assembly my data (plant genome about 380 Mb,Hiseq 2000, 101 bp reads, totally 139 million paired end reads). At first, I trimmed the low quality reads and adapter contaminated reads , after trimming, the average reads quality is above 20 revealed by fastqc.
But the assembly result from minia is strange, I tried Kmer 31,35, 39, 43, from the assembly results, most contigs started with ploy A (about twenty bp), and with the Kmer grow bigger,the GC content grows down . Does anyone face things like that?
Thank you!
yun
I am a newbie in de novo assembly. I just used software minia 1.4683 to assembly my data (plant genome about 380 Mb,Hiseq 2000, 101 bp reads, totally 139 million paired end reads). At first, I trimmed the low quality reads and adapter contaminated reads , after trimming, the average reads quality is above 20 revealed by fastqc.
But the assembly result from minia is strange, I tried Kmer 31,35, 39, 43, from the assembly results, most contigs started with ploy A (about twenty bp), and with the Kmer grow bigger,the GC content grows down . Does anyone face things like that?
Thank you!
yun
Comment