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Remove Duplicate Reads From Fasta File

Hi all,

I want to remove duplicate reads from my fasta file. I tried to use fastx_collapser. But since my reads contains lowercase letters and hyphens it failed.

Please help.

Thanks,D.

fasta read
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updated by Eslam Samir Eslam Samir • written by deepthithomaskannan deepthithomaskannan

It's like everybody wants to remove duplicates here!

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written by Manu Prestat Manu Prestat

3 answers

Try the sequniq tool from the GenomeTools suite:

gt sequniq -o output.fasta input.fasta
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written by Manu Prestat Manu Prestat

i tried this command, plz could u tell how this command applied...

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written by Kumar Kumar

Try CD-hit or Uclust

You can remove unwanted hyphens and convert to uppercase using sed:

echo FaSta-TEst | sed "s/-//g ; s/(.*)/\U&/g"

• 2 views • link
written by Rm Rm

Or just tr: echo FaSta-TEst | tr -d - | tr 'a-z' 'A-Z'

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written by Ketil Ketil

Here is my free program on Github Sequence database curator (https://github.com/Eslam-Samir-Ragab/Sequence-database-curator)

It is a very fast program and it can deal with:

  1. Nucleotide sequences
  2. Protein sequences

It can work under Operating systems:

  1. Windows
  2. Mac
  3. Linux

It also works for:

  1. Fasta format
  2. Fastq format

Best Regards

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written by Eslam Samir Eslam Samir

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