I have been struggling to get my head around how to create Scaffolds. I have created a de novo Metatranscriptome assembly using single end sequences, which has yielded me about 260,000 contigs with a good statistics.I have blasted the output to reference genome. From here I am attempting to make the scaffolds. My aim to make scaffolds from my assembly is to make a pseudo-molecule.
I am wondering if people can share their thoughts and suggest some good ideas or tools which can make me accomplish this challenge on galaxy or using small script on python.
Thanks in advance