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SGA-ICE | Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly

Implements iterative error correction by using modules from String Graph Assembler (SGA). SGA-ICE is an iterative error correction pipeline that runs SGA in multiple rounds of k-mer-based correction with an increasing k-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads.

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Jeremie Vidal-Dupiol's avatar image

Jeremie Vidal-Dupiol

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I used SGA-ICE to correct illumina shotgun sequencing before de novo genome assembly. The results was in accordance with my expectation. I recommend !

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SGA-ICE classification

SGA-ICE specifications

Unique identifier:
OMICS_14851
Software type:
Pipeline/Workflow
Restrictions to use:
None
Input format:
FASTQ
Biological technology:
Illumina
Programming languages:
Python
Computer skills:
Advanced
Requirements:
SGA
Name:
SGA-Iteratively Correcting Errors
Interface:
Command line interface
Input data:
The read data.
Output data:
A shell script that contains all commands to run iterative error correction of the given read data with the given parameters.
Operating system:
Unix/Linux
License:
MIT License
Stability:
Stable
Maintained:
Yes

SGA-ICE distribution

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SGA-ICE support

Documentation

Maintainer

  • Michael Hiller <>

Credits

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Publications

Institution(s)

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

Funding source(s)

This work was supported by the Max Planck Society and fellowship 2012/01319-8 from Fundaçao de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP).

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