First run through assembly of a mitochondrial genome sequenced with MiSeq (2 x 250) gave a pretty poor assembly with Kmers 25 through 31 (results shown for K31 - the best of the four). For comparison, Newbler gave two scaffolds which nearly covered the whole genome.
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Assembly id: 4
Assembly score: 98
Velveth timestamp: Jul 5 2015 01:30:15
Velvetg timestamp: Jul 5 2015 01:46:28
Velveth version: 1.2.02
Velvetg version: 1.2.02
Readfile(s): -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velveth parameter string: auto_data_31 31 -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velvetg parameter string: auto_data_31 -clean yes
Assembly directory: /home/farman/auto_data_31
Velvet hash value: 31
Roadmap file size: 33431342
Total number of contigs: 16825
n50: 98
length of longest contig: 275
Total bases in contigs: 1568075
Number of contigs > 1k: 0
Total bases in contigs > 1k: 0
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Second round optimization with K31 failed to generate an assembly at all:
Final optimised assembly details:
********************************************************
Assembly id: 4
Velveth timestamp: Jul 5 2015 01:30:15
Velvetg timestamp: Jul 5 2015 02:09:33
Velveth version: 1.2.02
Velvetg version: 1.2.02
Readfile(s): -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velveth parameter string: auto_data_31 31 -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velvetg parameter string: auto_data_31 -clean yes -exp_cov 3 -cov_cutoff 0.3502176
Assembly directory: /home/farman/auto_data_31
Velvet hash value: 31
Roadmap file size: 33431342
Total number of contigs: 0
n50: 0
length of longest contig: 0
Total bases in contigs: 0
Number of contigs > 1k: 0
Total bases in contigs > 1k: 0
Paired Library insert stats:
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Anyone know what's going on here? As an aside, I'm planning to increase max kmer size to run an optimization with k75 through k125 but I'm concerned that the assembly isn't working as it should to start off with. Note that I need to switch to a de Bruin assembler because most of our assemblies are too large for Newbler to handle and I'm using the mitochondrial data to optimize settings.
********************************************************
Assembly id: 4
Assembly score: 98
Velveth timestamp: Jul 5 2015 01:30:15
Velvetg timestamp: Jul 5 2015 01:46:28
Velveth version: 1.2.02
Velvetg version: 1.2.02
Readfile(s): -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velveth parameter string: auto_data_31 31 -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velvetg parameter string: auto_data_31 -clean yes
Assembly directory: /home/farman/auto_data_31
Velvet hash value: 31
Roadmap file size: 33431342
Total number of contigs: 16825
n50: 98
length of longest contig: 275
Total bases in contigs: 1568075
Number of contigs > 1k: 0
Total bases in contigs > 1k: 0
**********************************************************
Second round optimization with K31 failed to generate an assembly at all:
Final optimised assembly details:
********************************************************
Assembly id: 4
Velveth timestamp: Jul 5 2015 01:30:15
Velvetg timestamp: Jul 5 2015 02:09:33
Velveth version: 1.2.02
Velvetg version: 1.2.02
Readfile(s): -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velveth parameter string: auto_data_31 31 -longPaired -fastq SSFL14_mitochondrion/SSFL14-3_mitochondrial_reads.fastq
Velvetg parameter string: auto_data_31 -clean yes -exp_cov 3 -cov_cutoff 0.3502176
Assembly directory: /home/farman/auto_data_31
Velvet hash value: 31
Roadmap file size: 33431342
Total number of contigs: 0
n50: 0
length of longest contig: 0
Total bases in contigs: 0
Number of contigs > 1k: 0
Total bases in contigs > 1k: 0
Paired Library insert stats:
**********************************************************
Anyone know what's going on here? As an aside, I'm planning to increase max kmer size to run an optimization with k75 through k125 but I'm concerned that the assembly isn't working as it should to start off with. Note that I need to switch to a de Bruin assembler because most of our assemblies are too large for Newbler to handle and I'm using the mitochondrial data to optimize settings.
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