Tools that extract insert sequences?
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
1 answer
$ 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.
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