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Table 2 Installation information and parameter settings of the different programs

From: LSCplus: a fast solution for improving long read accuracy by short read alignment

Tools Dependencies Parameters Complexity
LSCplus Bowtie2 (integrated) Few and easy to understand A compressed file. Download, uncompress and run.
LSC Aligner (not integrated) (bowtie2/bwa/novoalign/razers3) Few and easy to understand Install the Aligner and set the PATH. A compressed file. Download, uncompress and run.
PacBioToCA AMOS package (AMOS depends on many other programs) Few and easy to understand Source code or binaries. Strict requirements regarding the format of input content.
proovread Perl 5.10 or later,
Log::Log4perl,
Blast-2.2.24+ or later,
samtools-1.1 or later,
BLASR (integrated)
Many and specialized Source code needs to be compiled and depends on many other libraries.
LoRDEC gcc version 4.5 or newer, Boost C++ libraries,
GATB Core library.
Many and specialized Source code needs to be compiled and depends on many other libraries. The steps are cumbersome and error-prone.