Example commands
The command below is a mixed assembly, where a set of paired reads, available in two files with one member of each pair in each file, is used for all stages of the assembly, and a set of 454 data is used for guidance only. The output file, containing the fasta formatted assembled contigs, will be called myContigs.fasta.
Note the use of the -p no before the non-paired, 454 data. This ensures that the assembler knows that the data about to be entered are not paired. It effectively overwrites the earlier -p information provided earlier in the command.
clc_assembler -o myContigs.fasta -p fb ss 200 400 -q -i pairedRead-member1.fastq
pairedRead-member2.fastq -g ignore -p no -q 454read.sff
The above command is equivalent to:
clc_assembler -o myContigs.fasta -g ignore -p no -q 454read.sff -g use
-p fb ss 200 400 -q -i pairedRead-member1.fastq pairedRead-member2.fastq
Examples of undesirable commands
A command like the following would imply that the data in 454reads. sff was paired, in an interleaved file, with the reads having relative orientation of forward-reverse, and a paired distance range of 200 to 400 bases. That is, the earlier information provided to the -p parameter would be used for all the following data entered in the command.
clc_assembler -o myContigs.fasta -p fb ss 200 400 -q -i pairedRead-member1.fastq
pairedRead-member2.fastq -g ignore -q 454read.sff
A command like the following would fail because all reads are now used in a guidance only role. This leaves no reads being used to create the graph fragments in the initial stage. The reason here is that the -g ignore parameter is given early in the command and because not -g use parameter is entered later, all read
sets are ignored for the building of the fragments.
clc_assembler -o myContigs.fasta -g ignore -p no -q 454read.sff -p fb ss 200 400 -q
-i pairedRead-member1.fastq pairedRead-member2.fastq