Asking for help on SOAPdenovo

[75mph]

Hello, guys, I am completely new in Linux Operation System and genomics software.
Recently I am learning to use SOAPdenovo. I had downloaded the latest version of SOAPdenovo (1.05), and unpacked it, and also type"make" and "make install" to install it.
After that, I was also prepared the config file.
then, I just type "./SOAPdenvo"
computer says: "

Usage: SOAPdenovo <command> [option]
pregraph construction kmer-graph
contig eliminate errors and output contigs
map map reads to contigs
scaff scaffolding
all doing all the above in turn

then, I type "./soapdenovo all -s config_file -o output_prefix"
but the computer only says: "bash: ./soapdenovo: No such file or directory"

therefore, I had tried all that I can, but the software just cannot run properly. So Please tell me how to get it started properly!

Just thanks so much for help!

[Petrichor]

Hi there!

I just started with it myself so i can help you with the first steps.

First you need to create a config-data on your own (Read the MANUAL for further information).
Then you can start running the whole programm very simple.

You need to change directory to the folder, it should look something alike:
cd r223/bin/
there should be the two datasets namely SOAPdenovo-127mer and SOAPdenovo-63mer

Then you can start it like the following:
./SOAPdenovo-63mer all -s file.config(the config-file you create) -o filename(somename you give the programm, so it can save all the outputdata with this name) -K INT (the k-mer size you want) 1>name_for_the_errorreport_data.err 2>name_for_the_logdata.log

I hope this may help.

Best regards,
Petrichor.

[mgbfx9]

I am new in the field, just started using SOAP de novo for assembly.

I made the config file. My data are in *.fastq.gz format. These are paired end sequences, ran in Illumina MiSeq.
Do I have to unzip all files to run on SOAP denovo?
Do I have to change my data from *.fastq.gz format to .fa or fasta format, as the config file command below has both .fq and .fa formats?

q1=/path/**LIBNAMEA**/fastq1_read_1.fq

f1=/path/**LIBNAMEA**/fasta1_read_1.fa

Also in config commands, there are commands for single reads, but I have paired end reads, do I have to run this line?

#fastq file for single reads
q=/path/**LIBNAMEA**/fastq1_read_single.fq

Thanks,

[mastal]

If you have paired-end data in fastq format, just use the versions of the commands for paired-end data and fastq. Fastq is a standard format for NGS data.

[mgbfx9]

If you have paired-end data in fastq format, just use the versions of the commands for paired-end data and fastq. Fastq is a standard format for NGS data.

Thank you, mastal, for your suggestion.

[mgbfx9]

Hi,

I am having issues in running SOAPdenovo, I need help, so I am writing in details.

I downloaded the following SOAPdenovo file,

http://superb-dca2.dl.sourceforge.net/project/soapdenovo2/SOAPdenovo2/src/r240/SOAPdenovo2-src-r240.tgz

Next, I followed their instructions,
1.Installation:
You can download the pre-compiled binary according to your platform, unpack using "tar -zxf ${destination folder} download.tgz" and execute directly.

My command: $ tar -zxf /home/mydirectory/SOAPdenovo2-src-r240.tgz

2.Configuration file: I made my configuration file according to their instruction

3. I used the following command from my soapdenovo dir to run the program
$ {bin} all -s myconfig_file -K 63 -R -o graph_prefix 1>ass.log 2>ass.err

I can see the 2 files, but when I checked ass.err file, I get bash
$ cat ass.err
-bash: {bin}: command not found

Where did I do wrong ?

Many thanks in advance.