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. |