SOAPdenovo: what is the input file of the second step (the command "contig") ?

Question

[alecloic]

Hello

I am currently working on a de novo large genome assembly. In this context I would like to use the Soapdenovo program that seems to be very effective.

To verify that everything works fine, I chose to run the assembly process step by step. The first step is:

./SOAPdenovo-63mer sparse_pregraph -s /data/DataSet/DeNovo/Project_BombusImpatients/DataTrimming/trimming2/Correctreads/example.config -K 50 -z 250000000 -R -o graph_prefix 1>pregraph.log 2>pregraph.err

And the output files are:

edge_cvg_stat.txt       
graph_prefix.path
edge_len_stat.txt       
graph_prefix.preArc
edge_num_stat.txt       
graph_prefix.preGraphBasic
graph_prefix.edge.gz    
graph_prefix.sparse.edge
graph_prefix.ht_content 
graph_prefix.vertex
graph_prefix.ht_idx      
pregraph.err
graph_prefix.kmerFreq   
pregraph.log
graph_prefix.markOnEdge

This seems normal since most of are found in the section "Output files from the command pregraph " on the website.

The second step is:

${bin} contig -g `graph_prefix` -R 1>contig.log 2>contig.err

but I do not understand what is the input file graph_prefix since I have several files like graph_prefix.*

Does anyone know which files are to be used as input file in the second step?

Thank you

Cordially

Answer 1

[Renesh]

Your command is right for step 2. The output generated from step 1 will be used as input for step 2. you don't need to specify any input files for step 2. But all of your output from step 1 should be in same directory from where you are running command.

[alecloic]

it's good, it works. it was simple. I do not know why I tried to specify the input files in the second step.
thank you for your help.