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Error correction in sequence Assembly

hello,
Is that the error correction algorithms like Coral and Echo use a reference genome for the correction of errors? or they use the Denovo method?

Thank you for your reply

assembly error correction algorithms
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updated by Ram Ram • written by midox midox

Are you asking about correcting a genome assembly or correcting unassembled sequence reads? It might help to expand your post to indicate these things and whether or not you are interested only in the two programs you mentioned.

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written by SES SES

I found these two algorithms of error correction.

I have unassembled reads and I search in errors correction algorithms to correct these reads (based on alignment or MSA).

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updated by Ram Ram • written by midox midox

See here. There are also two review papers on that page.

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updated by Ram Ram • written by lh3 lh3

2 answers

A recent review paper: Correcting Illumina data

Key Points

  • Error correction is essential for improving Illumina sequencing data before using it in applications.
  • Existing correcting programs are effective, recovering an important amount of erroneous data, yet significant room for improvement remains.
  • Recommended programs:
    • HiSeq data: BLESS, Musket, RACER and SGA
      • MiSeq data: RACER
      • Human data: Musket, RACER and SGA.
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updated by Ram Ram • written by rtliu rtliu

For human data, the best tools are lighter and the latest bless. The old bless evaluated in the paper wasn't very good.

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updated by Ram Ram • written by lh3 lh3

Why not read the papers and figure that out yourself? Here they are.

Coral - Correcting errors in short reads by multiple alignments

ECHO: A reference-free short-read error correction algorithm

Let us know what you find.

• 0 views • link
updated by Ram Ram • written by Neilfws Neilfws

Thank you for articles.

In ECHO and CORAL without reference sequence they use the DeNovo method.

Do you know other error correction algorithms? I searched and did not find.

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updated by Ram Ram • written by midox midox

BBTools has an error correction tool, BBNorm (which does denovo normalization and/or error-correction). It's run like this: ecc.sh in=reads.fastq out=corrected.fastq.

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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