FILES
- example.fq.gz contains 10,000 70 bp sequences in FASTQ format (solexa encoding). 
  Sequences are metagenomic reads from a stool sample.

- example.fa.gz contains 10,000 500 bp sequences in FASTA format. 
  Sequences are simulated shotgun reads from the bacterial genome Treponema pallidum.

* These are toy datasets. In practice, between 300,000 to 500,000 reads are needed 
  for accurate estimates of average genome size for most metagenomes

SETUP
Add src directory to your PATH: export PATH=$PATH:/your_install_dir/MicrobeCensus/src 

EXAMPLES
1. Run with default options using either FASTA or FASTQ input files

microbe_census example.fq.gz fastq_example.out
   or
microbe_census example.fa.gz fasta_example.out

2. Run with recommended quality filtering options if sequences are in FASTQ format
    -filter exact duplicates (-d)
    -filter reads with an unknown base-call (N) (-u 0)
    -filter reads with mean quality < 5 (-m 5)

microbe_census -d -u 0 -m 5 example.fq.gz fastq_example.out


3. Run with different number of reads and read length

microbe_census -n 1000 -l 500 example.fa.gz fastq_example.out



