- Lab1: Preperations
-
Lab2: Analzying sequences, generating phylogenetic trees, and identifying sequences using BLAST
-
Tools: Biophython, BLAST, matplotlib
-
Lab3: Determine statistics on word occurences and Zipf's law
-
Tools: matplotlib
-
Lab4: Investigate and document the relationships between genes, enzymes and pathways
-
Tools: SQL(sqlite3), pandas, Biopython, entrez
-
Lab5: Obtain secondary structures of folded RNA investigate riboswitch scenarios in the paper by Penchovsky and Breaker
-
Tools: RNAfold
-
Lab6: Run bowtie analysis on strains of Shewanella oneidensis, solving contamination and analyzing coverage statistics
-
Tools: bowtie2, samtools, matplotlib
-
Lab7: Investigate compression algorithms on generated binary and fasta files and real biological information
-
Tools: numpy, matplotlib, gzip, bzip2, pbzip2, ArithmeticCompress, entrez
-
Lab8 & 9: Assemble genome de novo using PacBio and Illumina reads, extract quality statistics, identify taxonomic origin, and obtain two genome annotations via different pipelines
-
Tools: spades, assembly-stats, rna_hmm3, bedtools, SeqMatch, BASys, RAST