Extend from the known sequence as a starting point using a fastq file

Question

[nakanomasayuki265]

I wanted to extend a specific sequence using fastq file obtained by whole genome shotgun sequencing.

I think the grep command enables to search the sequences matching the sequence of interest. What kind of scripts can I repeat grep continuously using the matched sequence and then assembly these sequences? Are there any software to achieve these operation?

[Brian Bushnell]

It is not clear what you are trying to do. Can you please explain it in detail? Grep is not useful for genome assembly.

[shenwei356]

May be you can assemble all reads and then "grep".

[Petr Ponomarenko]

Could you please specify genome size, length and quality of reads obtained, whether these are paired end reads in fastq file and what is the goal of your research. Have you checked for contamination with bacterial and human genomes? Is it ancient or highly degraded DNA?

[Jenez]

Some assemblers such as spades allows you to input what's called 'trusted contigs' which I guess might fulfil your needs? Run an assembly of the sequence reads and input your existing fasta sequence as a trusted contig.