Regarding opening of fastq whole genome data file and its assembly

Question

[Shakunthala Natarajan]

1. I have two 3.7 GB whole genome data files (read 1 and read 2) of whole genome data obtained by paired end sequencing in fastq format. I am unable to open the fastq file in gedit in ubuntu. It takes a lot of time to be opened by gedit and after sometime it shows, file too large to be opened by gedit and system has low memory. My system memory is 12 GiB. Can someone please let me know how to open the fastq files using gedit or any other text editor?
2. How can I convert fastq file to fasta file?
3. I am planning to use SOAPdenovo2 for genome assembly. Can someone please help me with how to use both the read 1 and read 2 fastq files for assembly using SOAPdenovo2?
4. Is my system suitable to carry out genome assembly using SOAPdenovo2? Kindly let me know.

Thank you!

Answer 1

[Ram]

Get a bioinformatician - someone with experience processing High Throughput Sequencing (aka NGS) datasets. FASTQ files are not meant to be opened using gedit. 12 GB is insufficient RAM to do alignment/assembly. If you're attempting to do this on your own, read as much as you can before starting, and use Galaxy instead of running things on your local machine.

Answer 2

[Mensur Dlakic]

• There is no need to open .fastq files, because usually there is no need to edit them manually.
• SOAP has a utility called fq2fa which will convert a .fastq file to .fasta
• If you use SOAP it may be possible to assemble this with the RAM you have. There are tutorials on SOAP web page regarding the assembly. Generally speaking, 12 Gb of RAM is not enough for most assembly applications. You may want to try MIRA instead if this is a single genome.

http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html