SOAPdenovo2

[pari_89]

Hello everyone, I am new to this forum and new to using assembly tools as well. I am trying to use SOAPdenovo2 and tried to write the configuration file which is as follows :

#maximal read length
max_rd_len=36
[LIB]
#average insert size
avg_ins=100
#if sequence needs to be reversed
reverse_seq=0
#in which part(s) the reads are used
asm_flags=3
f=sample.fq

I am using soapdenovo2 in steps. I tried to use the pregraph_sparse63mer version using this command :

/pregraph_sparse63mer -s configfile -K 63 -z 1000000 -o output_graph -p 4


The programs starts to build the graph but no nodes are allocated and it seems to parse the file but O kmer detected etc...

I have tried with combinations of -k 23 and smaller values because my reads are very short (36 nt) in length and it is a bacterial file 88 MB

I do not know if my parameters are correct in the config file but I am using only ONE FASTQ file.

Thank you.

[mastal]

SOAPdenovo2

If the file with your reads is in fastq format you should have
q=sample.fq

in the configuration file.

Did you get any better results with -K 23 or smaller?
Kmer size needs to be shorter than your reads.

[pari_89]

Hi, Thank you. Yes, it started to construct the graph and when I used the command soapdenovo2 63-mer contig -g output_graph , it produced a file named output_graph.contig

However, the contigs are very small and in this format:

>1 length 16 cvg_0.0_tip_0
AAAAAAAAAAAAAAAA

is that alright?

I used the same pregraph_sparse command but used -K 15

[Scaon]

SOAPdenovo2

Hi,

A month ago, i was struggling with pregraph_sparse too.
My problem was, as you stated "The programs starts to build the graph but no nodes are allocated and it seems to parse the file but O kmer detected etc..."

I compiled from source in the first place. Then, i decided to give binaries a try, and it was finally working. Maybe this could solve your issue.

Best,
Erwan

[pari_89]

Hi thank you, I compiled from the source and the program is working but the length of the contigs are in the format that I stated above and does not seem right. Have you used Soapdenovo2 and are your contigs in the same format?

Thank you.