What is deep sequencing? People talk about deep sequencing. Is there any way to calculate how deep the sequencing is ? What should be the optimum depth to get reliable data ?

I am doing whole genome sequencing of a virus genome which is 10 kb long. I got 80000 reads from Illumina sequencing. Is there any way to tell about my sequencing depth ?
I found a post useful for this topic.

It explains the difference of coverage and depth.  It also has a useful explanation on how to calculate coverage and depth.



Here is a copy of what the link says just encase the post is removed:


  Depth of coverage
  
  How strong is a genome "covered" by sequenced fragments (short reads)? 
  
  Per-base coverage is the average number of times a base of a genome is
  sequenced. The coverage depth of a genome is calculated as the number
  of bases of all short reads that match a genome divided by the length
  of this genome. It is often expressed as 1X, 2X, 3X,... (1, 2, or, 3
  times coverage).
  
  Breadth of coverage
  
  How much of a genome is "covered" by short reads? Are there regions that are not covered, even not by a single read? 
  
  Breadth of coverage is the percentage of bases of a reference genome
  that are covered with a certain depth. For example: 90% of a genome is
  covered at 1X depth; and still 70% is covered at 5X depth.


SAMtools: get breadth of coverage

Get breadth of coverage of a reference genome. 

How many bases of my reference genome are covered by my short reads sample at a level of 5X or higher?

 # set shell variables to your file-names

 REF_GENOME_FILE=my_ref_genome.fna
 WGS_SAMPLE=my_short_read_sample.fastq 
 MIN_COVERAGE_DEPTH=5



Map short reads against reference genome (bowtie2)

# create bowtie2 index database (database name: refgenome)

bowtie2-build ${REF_GENOME_FILE} refgenome
ls
refgenome.1.bt2
refgenome.2.bt2
refgenome.3.bt2
refgenome.4.bt2
refgenome.rev.1.bt2
refgenome.rev.2.bt2


# map reads and sort bam file
bowtie2 -x refgenome --no-unal -U ${WGS_SAMPLE} -S - -p 12 | \
samtools view -bS - | \
samtools sort -m 5G - mapping_result_sorted.bam

-U ${WGS_SAMPLE} consider all reads as unpaired reads
-S -             bowtie output in SAM format, write to standard out
-x refgenome     use reference genome bowtie2-database
--no-unal        suppress SAM records for reads that failed to align
-p 12            use 12 processors

Get breadth of coverage (SAMtools)

# create samtools index
samtools index mapping_result_sorted.bam

# get total number of bases covered at MIN_COVERAGE_DEPTH or higher
samtools mpileup mapping_result_sorted.bam | awk -v 
X="${MIN_COVERAGE_DEPTH}" '$4&gt;=X' | wc -l
32876

# get length of reference genome
bowtie2-inspect -s refgenome | awk '{ FS = "\t" } ; BEGIN{L=0}; {L=L+$3}; 
END{print L}'
45678



Result: breadth of reference genome coverage
total number of covered bases: 32876  (with >= 5X coverage depth)
Depth of coverage (average per-base coverage): 0.719 X (32876 ÷ 45678) (total number of covered bases divided by reference genome length)
percent: 71.9%  (0.719 × 100) (coverage breadth in percent)