Dava

Dear all I am new in this field. in need more clarified information about configuration file contents. in the manual: "Parameters for the bowtie2, mateAn, nucmer, asseMerge, and meta2fasta programs can be specified" is that mean some parameters of all of these programs should specified mandatory or few of them depending on the purpuse or data that i have ? for example i have A assemly (bowtie2 aligned PE illumina sequencing reads to pacbio long read sequence assembly and improved by pilon) and B...