I have a list of >100 circular contigs that I would like to remove from my de novo genome assembly.fasta. How can I remove these contigs from the assembly.fasta using a text file with the contig names/numbers? Or is there another way?
•
written
by
kristina.mahan
1 answer
If you already know which contigs are circular, you can use the really cool seqkit tool. The grep subcommand is the perfect tool for this job.
seqkit grep assembly.fasta -n -v -f circular_contigs.txt > assembly_clean.fasta
-n specifies to match by full name not just by id pattern (this means the names need to match 100%)
-v inverts the search criteria (i.e. anything that's not circular)
-f specifies the file by which to look for patterns (in this case the circular contig header names)
circular_contigs.txt is a list (one header per line) that identifies the circular contigs to be removed
> assembly_clean.fasta seqkit outputs to the terminal (stdin) so this last bit is piping into a new file
More info here: https://bioinf.shenwei.me/seqkit/
Hope that helps
Log in to answer this question.
-
How to automate blasting contigs?
written by marongiu.luigi
-
Copy number (repeat count) of de nove assembly contigs
written by Caronkey •
-
de novo genome assembly of bacterial genome
written by rthapa •
-
Generate single genome consensus fasta file from SPAdes output: viral genome sequencing
written by snow_seq •
-
How to extract variable nucleotide regions from a list of contigs
written by kayrouz.1 •
-
Inferring most probable integer copy number (repeat count) of contigs of a draft genome
written by misaghb •
-
Move And Renumber The Origin Of Circular Genome
written by ivpz •
-
Assessing Quality And Accuracy Of De Novo Genome Assembly
written by a81526a •
-
Tools For Visualizing Rna-Seq Splicing Graphs From De Novo Assembly Without A Reference Genome?
written by Tianyang Li •
-
Snp Detection And Genotyping In Ngs (Next Generation Sequencing)
written by Eric Normandeau
