dereplication process in metagenomics

Question

[sacha]

Hi,

Could you explain briefly what's the goal of the "dereplication" process in a metagenomics analysis ?

Answer 1

[sacha]

I think I understood the purpose ! Derepliaction is not a filtering process ! This step is used to compute the abundance of reads.
For instance, I have the following fasta file :

> seq1 
ACGT
> seq2 
ACGT
> seq3 
TCGA
> seq4 
GGAC

After dereplication I will have :

> seq1_2
ACGT
> seq3_1
TCGA
> seq4_1
GGAC

Note that abondance value are written in the name of sequence

[sacha]

For instance, using vsearch :

>A1
AGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCA
>A2
AGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCA
>A3
AGATACAGAGTAGAAAGTAGAGATCAGATGAGTAGATGATAGATACCCCCCCCCCCCTTTTTCCCCCCAAATAGTGTACCATATGGTGATTATGCG
>A4
AGATACAGAGTAGAGAGAGTAGAGATCAGATGAGTAGATGATAGATAGCACACCATTGGATTGTACGTATTAGTGTACCATATGGTGATTATGCG
>A5
AGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCA

The following command will convert to :

vsearch --derep_fulllength test.fa --output derep.fasta --sizeout

>A1;size=3;
AGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCAAGATACCA
AGATACCAAGATACCA
>A3;size=1;
AGATACAGAGTAGAAAGTAGAGATCAGATGAGTAGATGATAGATACCCCCCCCCCCCTTTTTCCCCCCAAATAGTGTACC
ATATGGTGATTATGCG
>A4;size=1;
AGATACAGAGTAGAGAGAGTAGAGATCAGATGAGTAGATGATAGATAGCACACCATTGGATTGTACGTATTAGTGTACCA
TATGGTGATTATGCG