Filter contig fasta file by GC content
Hello!
I have a de novo built contig file (contigs.fasta), assembly is done in SPAdes. From this file, I need to extract only the node sequences which have GC content below a certain % (e.g. extract all the node sequences that have GC content < 35%).
Do you have any suggestions of how I can do this? I am currently using seqkit to show me the GC content % of each node:
seqkit fx2tab --name --only-id --gc contigs.fasta > results.txt
The problem is, this way I can only see GC% of each node, and cannot do any "extraction" of the actual node sequences I need.
Thank you very much in advance!
• 1,948 views
•
link
updated
by
GenoMax
•
written
by
victoriahristovaa •
•
written
by
victoriahristovaa •
1 answer
Log in to answer this question.
More posts like this
-
Bus error (core dumped) when Aligning contigs to the reference in QUAST
written by ManuelDB
-
Issues with bash script and seqkit and awk
written by Hosny.yasmine123 •
-
Mapping reads to a very small reference
written by victoriahristovaa •
-
About calculating the GC content in a sliding window
written by jon.brate
-
set the minimum contig length in spades
written by babdalhamid •
-
Writing a script for quast
written by babdalhamid •
-
De-novo assembly using SPADES
written by ram.mainali •
-
Transcriptome assembly: Low GC, short contigs, low read alignment
written by jmah •
-
Does SPades contigs.fasta contain unassembled reads?
written by ciclistadan •
-
How To Calculate Gc Content Of Each Contig In A Multifasta File
written by HG
