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.
#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.
Comment