Tools that extract insert sequences?

Question

[aveadj]

If I know the flanking sequences to the left and right, are there tools that can return a fasta/fastq file of just my insertion sequences?

example:

ABCDA

A = random sequence (may not exist) B = left flanking sequence C = insertion sequence I wish to extract D = right flanking sequence

Answer 1

[shenwei356]

seqkit amplicon

$ echo -ne ">s\nACCCGCCATTTTC\n" | seqkit amplicon -F CCC -R AAAA
[INFO] 1 primer pair loaded
>s
CCCGCCATTT

$ echo -ne ">s\nACCCGCCATTTTC\n" | seqkit amplicon -F CCC -R AAAA -r 4:-5
>s
GCCA

Also try 2FAST2Q, with a GUI.

[aveadj]

Thank you!