You can find the selected data here (the first link is the NCBI SRA link, the second is the EBI ENA  ftp link)

454 data: NCBI, EBI

Illumina data: NCBI, EBI read 1, EBI read 2

Ion Torrent data: NCBI, EBI

An informative video about E. coli (Source: IAQ Video Network):

Here is a list of bioinformatics related tasks I plan to discuss, not necessarily in this order  (links will be added later):

• Read preprocessing
  • File format conversion
  • Read quality control (1 and 2)
  • Quality filtering and trimming
  • Adaptor trimming
  • Demultiplexing
  • Random downsampling
• Reference
  • Indexing
  • Subsampling and statistics
• Targeted vs. whole reference alignment
  • Running the alignments (1, 2, 3)
  • Alignment statistics (coverage analysis, proper pairs…)
  • Manipulating an alignment file (format conversion, indexing)
  • Subsampling, getting reads/regions out of an alignment
  • Indel realignment
  • Quality recalibration
  • Duplicate marking
  • Sorting
  • Merging
  • Filtering
  • De novo, semi de novo assembly
  • Visualisation (sam/bam, de novo)
• Variant call
  • Available tools (GATK, Samtools, also smaller tools like VarScan,…)
  • Variant filtering
  • Variant effect prediction (known and unknown variants)
  • Visualisation
• Submitting to databases