Step 8: CAP3 assembly

CAP3 assembly is a simplest step in this pipeline.

We have run cap3 with default options on tomato_ABC.fasta file and redirected CAP3 output to tomato_ABC.cap3.out file:


$ cap3 tomato_ABC.fasta > tomato_ABC.cap3.out


It takes several hours for CAP3 to finish the assembly with this example file on a computer with 1 Gb of memory and 750 MHz CPU.

After CAP3 is done, several output files are generated:

tomato_ABC.cap3.out
tomato_ABC.fasta.cap.ace
tomato_ABC.fasta.cap.contigs
tomato_ABC.fasta.cap.contigs.links
tomato_ABC.fasta.cap.contigs.qual
tomato_ABC.fasta.cap.info
tomato_ABC.fasta.cap.singlets

We need only tomato_ABC.cap3.out file to find SNPs/INDELs in the assembly.