Hi there I'm having an issue working with the assembler velvet, hopefully someone knows what is happening.
I'm visualizing my assembly using Tablet by giving this software the AMOS file velvetg produces when using the option
-amos_file yes at the moment of the assembly. The problem is the number of contigs that Tablet shows me doesn't match the number of contigs in the actual contigs.fa text file of the same assembly (Tablet shows about 100 contigs more). At first I thought the AMOS file wasn't filtering the contigs with less than 500 nucleotides that were filtered in the text file since I stated the option
-min_contig_lgth 500 when using velvetg, however when I didn't use the filter I still got more contigs in tablet compared to the text file.
Is there something I'm missing about how the AMOS file works? Why is this happening? Thank you in advance.