# REAPRLong : A Tool to Scaffold and Quality Control genome assemblies using (low coverage) long reads
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### Dependencies/Prerequisites:
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@@ -24,36 +24,11 @@ Otherwise the script can be run using python directly: "python main.py ..."
The help function can be accessed via: ./main.py -h|--help and provides a general overview of how to use and which parameters can be set when using the tool.
REAPRLong needs a genome assembly in fasta format, long reads (e.g. PacBio or ONT) in fastq or fasta format and a path, where output files will be generated, as mandatory input to run. Additional parameters can be set but the default values are tested and generally provide the best results.
@@ -74,6 +49,6 @@ REAPRLong generates multiple output files in the specified output directory.
10. misjoins\_it\*.txt - identified misjoins (within the genome compared to the reads). The \* is an integer value indicating the iteration of QC, starting with 0 which represents the original assembly. Every subsequent number relates to the adjusted\_contigs\_it\*.fa of the previous iteration.