# falco 0.3.0


## Falco: FastQC Alternative Code

This program is an emulation of the popular FastQC software to check large
sequencing reads for common problems.

Location and version:

```console
$ which falco
/local/cluster/bin/falco
$ falco --version
falco 0.3.0
```

help message:

```console
$ falco --help
Usage: falco [OPTIONS] <seqfile1> <seqfile2> ...

Options:
  -h, --help                print this help file and exit
  -v, --version             print the program version and exit
  -o, --outdir              Create all output files in the specified
                            output directory. If notprovided, files
                            will be created in the same directory as
                            the input file.
  -C, --casava              Files come from raw casava output
                            (currently ignored)
  -n, --nano                Files come from fast5 nanopore sequences
  -F, --nofilter            If running with --casava do not sequences
                            (currently ignored)
  -e, --noextract           If running with --casava do not remove poor
                            quality sequences (currently ignored)
  -g, --nogroup             Disable grouping of bases for reads >50bp
  -f, --format              Force file format
  -t, --threads             Specifies number of threads to process
                            simultaneos files in parallel (currently
                            set for compatibility with fastqc. Not yet
                            supported!)
  -c, --contaminants        Non-default filer with a list of
                            contaminants
  -a, --adapters            Non-default file with a list of adapters
  -l, --limits              Non-default file with limits and warn/fail
                            criteria
  -T, --skip-text           Skip generating text file (Default = false)
  -H, --skip-html           Skip generating HTML file (Default = false)
  -S, --skip-short-summary  Skip short summary(Default = false)
  -q, --quiet               print more run info
  -d, --dir                 directory in which to create temp files
  -A, --advanced-mode       advanced mode: adds more information to the
                            FastQC output depending on non-fastqc user
                            flags
  -B, --bisulfite           reads are whole genome bisulfite
                            sequencing, and more Ts and fewer Cs are
                            therefore expected and will be accounted
                            for in base content (advanced mode)
  -R, --reverse-complement  The input is a reverse-complement. All
                            modules will be tested by swapping A/T and
                            C/G

Help options:
  -?, -help                 print this help message
      -about                print about message

```

falco should result in a speed-up over FASTQC but is still not completely a 1:1
replacement. Keep development in mind when using FASTQC.

software ref: <https://github.com/smithlabcode/falco>  
research ref: <https://doi.org/10.12688/f1000research.21142.2>