Remove Duplicate Reads From Fasta File

Question

[deepthithomaskannan]

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.

[Pierre Lindenbaum]

duplicate of:

How to remove the same sequences in the FASTA files?

[Manu Prestat]

It's like everybody wants to remove duplicates here!

Answer 1

[Manu Prestat]

Try the sequniq tool from the GenomeTools suite:

gt sequniq -o output.fasta input.fasta

[Kumar]

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

Answer 2

[Rm]

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"

[Ketil]

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

Answer 3

[Eslam Samir]

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