Reptile

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Description

reptile website  

Reptile is a software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. Reptile has several favorable properties:

  • Memory efficiency. Reptile can process input data with sizes larger than main memory. For instance, to process a 160x coverage (3.8GB) Illumina data for E. coli it requires only ~1GB memory, which is easily available in a desktop computer.
  • High speed. Processing Illumina data for a microbe typically takes 0.5hr ~ 2hrs, depending on the number and the quality of reads.
  • Can handle reads containing non-acgt characters and reads with non-equal length.
  • Makes simple use of quality score information.
  • Reptile has been developed by Xiao Yang, Karin Dorman and Srinivas Aluru.

Upstream documentation for reptile.

Required Modules

modules documentation

Serial and Parallel (OMP)

  • reptile

Parallel (OpenMP)

System Variables

  • HPC_REPTILE_DIR - installation directory
  • HPC_REPTILE_BIN - Executable directory
  • HPC_REPTILE_CONF - Sample configuration files

Additional Information

Make sure that the environmental variable OMP_NUM_THREADS is set to the number of threads you wish to use when executing Reptile when using the reptile-omp binary.

There is a reptile tutorial written by Daniel S. Standage.

The available binaries and scripts include:

fastq-converter reptile_merger reptile-omp reptile-omp-intel reptile-v1.1 seq-analy.

Sample configuration files are in $HPC_REPTILE_CONF



Citation

If you publish research that uses reptile you have to cite it as follows: X. Yang, K. Dorman and S. Aluru, “Reptile: Representative tiling for short read error correction”, Bioinformatics, 26(20), 2526-2533, 2010.

Validation

  • Validated 4/5/2018