Here, it is assumed that a previous step has placed multiple files in the repository named contig1.fa, contig2.fa, etc.The Unix-like glob contigs*.fa in the scatter field tells BayerCLAW to run the Annotate step on each of these files in parallel.When all of the branches are finished, paths to the output files are recorded in a JSON-formatted manifest file named after the name of the scatter . I've tried to work with prokka, but it seems not to generate the gbk file (neither the gbf one). FastQC generates a report to visualize problems associated with either the sequencer or the starting library. prokka - freesoft.dev #A script that automatically invokes prokka on a directory of FASTA genomes and neatly organises the output. PURPLE: A purity, ploidy and copy number estimator for whole genome tumor data: . You prokka annotated files will be in the folders FILE1.prokka.output (FILE1 here is your assemblies). "Genome assembly for artists" draft part 1 - Commonplace Lab Bacterial genome annotation using Prokka; Introduction to automation; K-mers, k-mer specificity, and comparing samples with k-mer Jaccard distance. BayerCLAW - Open-Source, Serverless Orchestrator for Scientific ... Everything from CDS, microRNAs, binding domains, ORFs, and more can be handled by this format. In this section we will use a software tool called Prokka to annotate the draft genome sequence produced in the previous tutorial.Prokka is a "wrapper"; it collects together several pieces of software (from various authors), and so avoids "re-inventing the wheel". Open the terminal (Ctrl+T) and type the following commands: $ sudo apt-get update. Remember, to use scp, you should open a new Terminal window that is NOT logged in to baross. PROKKA produces several types of output, such as: a GFF file, which is a standardised, tab-delimited, format for genome annotations; a Genbank (GBK) file, which is a more detailed description of nucleotide sequences and the genes encoded in these. . See which versions of Prokka are available: $ module avail prokka. Prokka is a pipeline for rapidly annotating prokaryotic genomes. Here what you are asking prokka to do is annotate the contigs in JY1305contig.fasta, name the contigs as if from a sequencing center named "U", make the annotations compliant with NCBI standards (necessary if you want other tools to read your files) and force an overwrite of previous iterations of a default-named output directory.