Data Sets¶
The datasets we will use are sequencing reads from M. tuberculosis genome generated using Illumina and PacBio platforms. For the Illumina platform, there are two sets of reads covering the same library at 20X and 60X coverage. We will also use a reference assembly for M. tuberculosis H37Rv (NC_000962.3). H37Rv genome is 4411532 bp long.
The datasets are located under /home/mtb_upm/mtb_genomics_workshop_data/genome-assembly-annotation/data directory, which has the following content:
| File | Content |
|---|---|
| MTB_illumina60X_R1.fastq | 60X coverage run, Illumina short reads, forward |
| MTB_illumina60X_R2.fastq | 60X coverage run, Illumina short reads, forward |
| MTB_illumina20X_R1.fastq | 20X coverage run, Illumina short reads, forward |
| MTB_illumina20X_R2.fastq | 20X coverage run, Illumina short reads, forward |
| MTB_pacbio_circular-consensus-sequence-reads.fastq | PacBio long reads, circular consensus sequence |
| NC_000962.3.fna | Mycobacterium tuberculosis H37Rv reference assembly, 4411532 bp, linear |