Hi,
I have just begun assembling some genomes using velvet using a range of kmer lenghts (a gap of 10 between kmer length of 25-179). For all of these files I am generating very large contigs.fa files - Mostly between 0.5-50 gigs.
Some general characteristics of the assemblies are an N50 of between 1000-5000 and a sum sequence of 30-50e6.
Here is an example of the command I am using to perform the assembly.
"velveth assembled155_qual 155 -fmtAuto -create_binary -shortPaired -separate FS10.raw.1.fastq FS10.raw.2.fastq
velvetg assembled155_qual -cov_cutoff auto -exp_cov auto -ins_length auto -read_trkg yes -amos_file yes"
Where each of the input files are approximately 1gig.
Whilst these the sum is quite large... I am not sure it should really equate to a 50gig .fa file...
Sorry if I have left out any info. Any help on this would be great!
Cheers
I have just begun assembling some genomes using velvet using a range of kmer lenghts (a gap of 10 between kmer length of 25-179). For all of these files I am generating very large contigs.fa files - Mostly between 0.5-50 gigs.
Some general characteristics of the assemblies are an N50 of between 1000-5000 and a sum sequence of 30-50e6.
Here is an example of the command I am using to perform the assembly.
"velveth assembled155_qual 155 -fmtAuto -create_binary -shortPaired -separate FS10.raw.1.fastq FS10.raw.2.fastq
velvetg assembled155_qual -cov_cutoff auto -exp_cov auto -ins_length auto -read_trkg yes -amos_file yes"
Where each of the input files are approximately 1gig.
Whilst these the sum is quite large... I am not sure it should really equate to a 50gig .fa file...
Sorry if I have left out any info. Any help on this would be great!
Cheers
Comment