The ReMILO manuscript is submitted to Bioinformatics!

ReMILO is software that detects misassembly errors in the contigs of a species using the corresponding short reads and the reference genome of a closely related species, as well as the corresponding long reads.

ReMILO is under the Artistic License 2.0.

1. System requirements

   ReMILO is suitable for 32-bit or 64-bit machines with Linux operating systems. At least 4GB of system memory is recommended for larger data sets.

2. Installation

   Aligners Bowtie2 and BWA-MEM are required to run ReMILO.

   • The source files in 'src' folder can be compiled to generate a 'bin' folder by running Makefile: make all.
   • Put Bowtie2, BWA-MEM and the 'bin' folder to $PATH: export PATH=PATH2Bowtie2:$PATH, export PATH=PATH2BWA-MEM:$PATH and export PATH=PATH2bin:$PATH, respectively.

3. Inputs

   • Contigs of a species assembled by any genome assembler (ABySS, ALLPATHS-LG, SOAPdenovo2, Velvet, etc.).
   • Reference genome from a closely related species.
   • Corresponding paired-end short reads in FASTA format.
   • Corresponding long reads in FASTA format (optional).

4. Using ReMILO

   runReMILO.py contigs.fa reference_genome.fa short_reads1.fa short_reads2.fa [-options | -options]
   

   Options (default value):
   -i/-insert n (500)
   Insert length of short reads.
   -k/-kmer n (19)
   Size of k bases.
   -d/-distance n (85)
   Minimum alignment distance of adjacent contig positions to detect a misassembly error (using either reference genome or long reads).
   -l/-longread long_reads.fa (yes)
   Corresponding long reads.
   -c/-coverage n (1)
   Minimum number of long reads required to detect a misassembly error.

5. Outputs

   • Misassembly locations. Each line of the file records the misassembly locations of one contig and has the following format : initial contig name : offset of first misassembly error; offset of second misassembly error ; ....
   • Split contigs at misassembly locations. Specification of each split contig has the following format: initial contig name : split contig ID, where the split contig ID starts from 0.
   • Remaining contigs without detected misassembly locations.