Greetings colleagues!
I am a second year Ph.D. student and I am currently taking a genome assembly class. We have been given a class project to de novo assemble a set of reads. The data set that we have been given contains mate pair reads from two generations of Illumina sequencing- some of the reads are 36bp and some of the reads are 76 bp. The professor of the class suggested that Velvet may produce different assemblies if I separate out the reads by size and do my assembly with the reads of different lengths in different files. However, as these sequences aren't actually long (capillary) reads, I can't figure out how to run velvet with all of that information.
The velveth command I think I would run (I'm doing this in Linux) is...
velveth [output directory] [kmer] -short -fasta short_forward.fa short_reverse.fa long_forward.fa long_reverse.fa -shortPaired short_shuffled.fa long_shuffled.fa -singletons short_singletons.fa long_singletons.fa
Is this correct? I haven't tried it yet, mind you, but I cannot conceptually understand how or if velvet would be able to use this information properly.
I have done the assembly with the data contained in single files successfully, but was hoping to generate something better if it's possible.
Thank you for considering my question!
I am a second year Ph.D. student and I am currently taking a genome assembly class. We have been given a class project to de novo assemble a set of reads. The data set that we have been given contains mate pair reads from two generations of Illumina sequencing- some of the reads are 36bp and some of the reads are 76 bp. The professor of the class suggested that Velvet may produce different assemblies if I separate out the reads by size and do my assembly with the reads of different lengths in different files. However, as these sequences aren't actually long (capillary) reads, I can't figure out how to run velvet with all of that information.
The velveth command I think I would run (I'm doing this in Linux) is...
velveth [output directory] [kmer] -short -fasta short_forward.fa short_reverse.fa long_forward.fa long_reverse.fa -shortPaired short_shuffled.fa long_shuffled.fa -singletons short_singletons.fa long_singletons.fa
Is this correct? I haven't tried it yet, mind you, but I cannot conceptually understand how or if velvet would be able to use this information properly.
I have done the assembly with the data contained in single files successfully, but was hoping to generate something better if it's possible.
Thank you for considering my question!
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