Bioinformatics (genomic project – alignment and homology researches X sequence assembly and genome annotation)

A genomic project. This project is a real case (albeit simplified) scenario.Use what you have learned to assemble and annotate the chloroplast genome present within the dataset (L1.fastq and R1.fastq,  310 Mb each). It might not be the only thing in there!
– Remember to filter the data, if required.
– You will have to select the kmer values for the assemblies. Use kmergenie to help you decide.
– Use a maximum of 8 processors for the assemblies (use Ray). This could take a long time, so I strongly suggest that you start this part of the assignment early. Make sure to use screen to run the analyses so that you can detach/re-attach (remember to source your .bash_profile).
– Once the assemblies are done, identify the chloroplast contigs by BLAST homology searches. Make your own database(s) then search against it using command line BLAST analyses. UsePlastidProteins.fasta to help you find the chloroplast contigs.
– Pull this/these contig(s) out in single fasta files.
– Use tRNAscan-SE and/or Aragorn to find tRNAs.
– Position rRNAs by using BLAST homology searches in pairwise mode (0). Use rRNAs.fasta as input for BLAST.
– Find the ORFs longer than 100 aa.
– Annotate using Artemis. Make sure that the ORFs start with a Methionine residue and end with a stop codon. Note that the protein-encoding petB, psaB, atpA and rRNA-encoding rrl genes will feature introns.
– Add locus_tags automatically with the Artemis built-in function. Use BIO550_ as the prefix and autoincrement by 10 with an initial value of 10 (i.e. BIO550_0010).
– Send the Artemis annotation files and a concise report describing the steps you did and any issues you might have encountered by email. Make sure to include all command lines you used in the report.

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