Velvet & paired-ends

[Thorondor]

if you don't want to compare paired end to single end you don't need to do "subsetting".

the last line just tells you your N50, how many reads were used (you can also request velvet to output a UnusedReads.fa file) etc, i am not sure if the number of nodes is the number of your contigs. You can check that by grep ">" -c contigs.fa.

[AdrianP]

Greetings to you all,

First of all thank you for creating this forum, it seems like a great way to share knowledge.

I am a undergraduate student starting on a job at my university involving assembly of sequenced data. I am an expirienced linux user so I will try to use linux programs.

Currently I have familiarized myself with velvet a bit and I wish to try to assemble some data that has been previously well assembled and I wanted to test velvets capabilities on it as well. After making sure I know how to use velvet I will also try Ray and SOAP.

So I have 2 files:
100611_s_4_1_seq_GDR-7.txt (1.6 GB)
100611_s_4_2_seq_GDR-7.txt (1.6 GB)

I have used this as a refrence for my work:

http://wiki.bioinformatics.ucdavis.edu/index.php/Illumina_assembly_using_velvet

From what I understand I need to merge the two files into 1 file with shuffleSequences_fastq.pl. Is this correct?

shuffleSequences_fastq.pl 100611_s_4_1_seq_GDR-7.txt100611_s_4_2_seq_GDR-7.txt 100611_s_4_both_seq_GDR-7.txt

I have trouble understanding what does subsetting mean from that page. If we look at:

17. Do the subsetting. Soon we will compare the single ended assembly to the paired-end assembly. In order for the comparison to be fair, we must use the same total number of reads. Therefore each paired end file will contain 1/4 of the reads:

It seems like they are trying to compare single ended with paired-end. I am only doing paired-end, do I need to do subsetting?

Final graph has 302039 nodes and n50 of 175, max 1779, total 5984104, using 13024530/17609332 reads

Now one more thing, after running velveth_de and velvetg_de, at the end of velvetg_de it tells me how many nodes have been created. Is that the number of contigs? How do I interpret that last line?

I am using the -shortPaired option for velveth.

My last question is, has anyone here used consed? I just wanted to ask since I have some problems setting up that program.

Thank you.