Some exercises to try ===================== 0. Finish or re-run one of the tutorials that you're particularly interested in. 1. Download and assemble some reads from the Short Read Archive (SRA) or elsewhere. Remember that `the ENA at EBI `__ offers FASTQ downloads of SRA sequence. (see these tutorials: :doc:`reads_and_qc` and `assembly-lab`) 2. Browse the `NCBI Bacterial genomes site `__, download a proteome of interest (you'll want the '.faa' files), and run the various BLASTs on 'em (e.g. find reciprocal best hits). See the instructions here: :doc:`tuesday`. 3. Map raw reads for the E. coli 0104 genome back to your assembly -- e.g. take the assembly at http://athyra.idyll.org/~t/ecoli-v41.fa and map the QC reads to it (see :doc:`bwa_mapping`). Bonus: load the resulting read mapping into Tablet. Bonus x 2: use the Prokka annotation .gff file to define features in Tablet. (If you didn't get all the way through the Prokka run, you can download a zip file of the results here: http://athyra.idyll.org/~t/ecoli0104-prokka.zip) 4. Assemble the provided ecoli reads *without* digital normalization. 5. Install BLAST and the ngs-scripts, and then try comparing an assembly with a genome by using the following commands:: blastall -i assembly.fa -d genome.fa -p blastn -e 1e-20 -o assembly.x.genome.blastn blastall -d assembly.fa -i genome.fa -p blastn -e 1e-20 -o genome.x.assembly.blastn python /usr/local/share/ngs-scripts/blast/calc-blast-cover.py genome.fa assembly.x.genome.blastn 300 assembly.fa python /usr/local/share/ngs-scripts/blast/calc-blast-cover.py assembly.fa genome.x.assembly.blastn 300 genome.fa 6. Try taking one of the assemblies (e.g. http://athyra.idyll.org/~t/ecoli-v41.fa) and mapping the QC reads used to assemble it back to it, to assess assembly completeness.