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#bioawk is a command-line gem; it’s an extension of awk that auto-assigns variables for BED, SAM, VCF, GFF, and FASTX[AQ] format files, speeding up routine tasks.

For FASTX:
$1:name
$2:seq
$3:qual (FASTQ only)
$4:comment

Found in @vsbuffalo’s great #Bioinformatics Data Skills.

#bioinformatics #bioawk @Vince Buffalo
in reply to Chase W. Nelson 倪誠志

Frank Aylward
Frank Aylward
• •
surprisingly, awk is something I never learned beyond the very basics, but I have heard that bioawk is a must
in reply to Frank Aylward

Chase W. Nelson 倪誠志
Chase W. Nelson 倪誠志
• •
@foaylward same situation exactly! I'm constantly writing scripts specifically so I can do routine tasks *at the command line* — this is just so great and flexible!
@Frank Aylward
in reply to Chase W. Nelson 倪誠志

Frank Aylward
Frank Aylward
• •
I can still remember the mantra "sed grep awk" from my intro bioinformatics prof....
in reply to Frank Aylward

Chase W. Nelson 倪誠志
Chase W. Nelson 倪誠志
• •
@foaylward same - I think I just ended up never using awk because it was too difficult to remember, or it was so much easier to do it other ways. My muscle memory pretty much amounts to cat | grep | sed | less :->
@Frank Aylward

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