The genome size and N50 of the genome is much smaller after polished for 2 times, the old polish tools such as pilon, after polishment, the genome and N50 will be a little bigger than before, and which type of snp/indel is changed?

[forrwill]

with tools wtpoa-cns for pacbio reads and Illumina reads.

[ruanjue]

Could you give the commands, genome size and N50?

[forrwill]

samtools-1.8/samtools view -@ 16 -O SAM Merge.bam | wtpoa-cns -t 16 -x sam-sr -d pecan_1.fasta -i - -fo pecan_2.fasta

[forrwill]

before: after 2 times polish

[ruanjue]

The images cannot be displayed

[forrwill]

[ruanjue]

I am afraid you need to paste text here, I still cannot display the image.

[forrwill]

before: Statistics: Scaffold Contig Total Number (#): 4116 4116 Total length (bp): 993692583 993692583 Gap(N)(bp): 0 0 Average Length (bp): 241421.91 241421.91 N50 Length (bp): 1184072 1184072 N90 Length (bp): 87150 87150 Maximum Length (bp): 6163683 6163683 Minimum Length (bp): 340 340 GC content : 36.28% 36.28%

after 2 times polish Statistics: Scaffold Contig Total Number (#): 4116 4116 Total length (bp): 958727807 958727807 Gap(N)(bp): 0 0 Average Length (bp): 232927.07 232927.07 N50 Length (bp): 1136923 1136923 N90 Length (bp): 83433 83433 Maximum Length (bp): 5909804 5909804 Minimum Length (bp): 328 328 GC content : 36.48% 36.48%

[ruanjue]

Thanks. Please select some tens of polished contigs to be compared with their original. Are the differences small indels or large? If you find there are many large indels on one contig, I am happy to debug on it later.

[forrwill]

while using Illumina reads for polishing, if the snps will be replaced?

[ruanjue]

Yes, wtpoa-cns -x sam-sr call consensus sequence from the multiple alignments of short reads.

[forrwill]

Thank you very much! I will compare some contigs at some time!