Hello All,
I am a graduate student trying to learn NGS as I wrap up my PhD. That said, we have sequenced our pet bacterial genome (Illumina HISeq 2500 PE 101 BP) and I have so far managed to produce what to me looks like a good assembly. Reads were cleaned up with trimmomatic and assembled using Ray-2.3.1 with a default kmer of 31. The output is as follows
Contigs >= 100 nt
Number: 28
Total length: 4963730
Average: 177276
N50: 246178
Median: 162206
Largest: 771798
Contigs >= 500 nt
Number: 28
Total length: 4963730
Average: 177276
N50: 246178
Median: 162206
Largest: 771798
Scaffolds >= 100 nt
Number: 22
Total length: 4965242
Average: 225692
N50: 338745
Median: 115189
Largest: 1908686
Scaffolds >= 500 nt
Number: 22
Total length: 4965242
Average: 225692
N50: 338745
Median: 115189
Largest: 1908686
The total length is in good agreement with other sequenced genomes of the same species (ranging 4.8-5.0 MB). But I am now beyond what anyone at my institute has experience with. I would like to go as far as possible towards closing the genome, but I am unsure what next steps to take. Can anyone provide some input as to what next logical steps I should take? Thank you very much!
I am a graduate student trying to learn NGS as I wrap up my PhD. That said, we have sequenced our pet bacterial genome (Illumina HISeq 2500 PE 101 BP) and I have so far managed to produce what to me looks like a good assembly. Reads were cleaned up with trimmomatic and assembled using Ray-2.3.1 with a default kmer of 31. The output is as follows
Contigs >= 100 nt
Number: 28
Total length: 4963730
Average: 177276
N50: 246178
Median: 162206
Largest: 771798
Contigs >= 500 nt
Number: 28
Total length: 4963730
Average: 177276
N50: 246178
Median: 162206
Largest: 771798
Scaffolds >= 100 nt
Number: 22
Total length: 4965242
Average: 225692
N50: 338745
Median: 115189
Largest: 1908686
Scaffolds >= 500 nt
Number: 22
Total length: 4965242
Average: 225692
N50: 338745
Median: 115189
Largest: 1908686
The total length is in good agreement with other sequenced genomes of the same species (ranging 4.8-5.0 MB). But I am now beyond what anyone at my institute has experience with. I would like to go as far as possible towards closing the genome, but I am unsure what next steps to take. Can anyone provide some input as to what next logical steps I should take? Thank you very much!
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