Genome assembly using Shasta
The third assembler we introduce is Shasta, a long-read assembler with very fast run-time that also produces contigs (in contrast to miniasms unitigs).
Change into directory assembler_practical/shasta. In contrast to the other assemblers Shasta expects fasta files as input, not fastq. Thus, before you can run Shasta you will have to convert the guppy fastq to a fasta file using the Shasta command FastqToFastq.py and then run shasta on the output fasta file.
FastqToFasta.py \ ~/course_data/practicals/basecalling_practical/all_guppy.fastq \ all_guppy.fasta shasta --input all_guppy.fasta
This will create a directory ShastaRun as output containing, among others, the assembly in fasta format (Assembly.fasta).
As before, assess the assembly using assembly-stats, dnadiff and Assemblytics.