** Overview                                                             :TOC:
   - [[#seq-frag----ref-based-simulation-of-readscontigs][seq-frag -- ref-based simulation of reads/contigs]]
   - [[#bio2svg----plot-bamgffbed-tracks-to-svg][bio2svg -- plot bam/gff/bed tracks to svg]]

** seq-frag -- ref-based simulation of reads/contigs
Simulate fragment libraries (Illumina SE/PE/MP, Pacbio, contigs) from reference
sequences. Errors models are not currently supported.
***** Dependencies
- [[https://github.com/BioInf-Wuerzburg/perl5lib-Fastq][perl5lib-Fastq]], [[https://github.com/BioInf-Wuerzburg/perl5lib-Fasta][perl5lib-Fasta]]
- [[http://search.cpan.org/~grommel/Math-Random-0.70/Random.pm][Math::Random]] 

#+BEGIN_SRC sh
cpanm Math::Random

# wherever you prefer
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git
git clone https://github.com/BioInf-Wuerzburg/perl5lib-Fasta.git

export PERL5LIB=/path/to/perl5lib-Fasta/Fastq:$PERL5LIB
#+END_SRC

***** Usage
#+BEGIN_SRC sh
seq-frag MODE -l LENGTH -c COVERAGE [options ..] < FASTA
# 50X 100bp single end reads
seq-frag se -l 100 -c 50 < genome.fa > read.fq
# 50X 100bp paired end, 180bp insert
seq-frag pe -l 100 -c 50 -i 180 < genome.fa | interleaved-split 1>reads_1.fq 2>reads_2.fq
# 50X mate pair, 2000bp insert
seq-frag mp -l 100 -c 50 -i 2000 < genome.fa | interleaved-split 1>reads_1.fq 2>reads_2.fq
# 20X pacbio style fragments, mean length 2000bp
seq-frag pacbio -l 2000 -c 20 < genome.fa > pb-reads.fq

# for more details
seq-frag --help
#+END_SRC

***** Sample
#+BEGIN_SRC sh
seq-frag mp -l 100 -c 1 -i 2000 ref.fa | interleaved-split 1> r_1.fq 2> r_2.fq
seq-frag mp -l 100 -c 1 -i 2000 -s ref.fa | interleaved-split 1> s_1.fq 2> s_2.fq
#+END_SRC

Mapped with [[https://github.com/lh3/bwa][bwa mem]] and visualized with [[https://www.broadinstitute.org/igv/][IGV]]:

[[etc/seq-frag-mp.png]]

** bio2svg -- plot bam/gff/bed tracks to svg
Plot mappings (bam), features and annotations (gff, bed) along sequences to high
quality SVGs.
***** Dependencies
- [[http://search.cpan.org/~ronan/SVG-2.33/][SVG-2.33]]

***** Usage
#+BEGIN_SRC sh
git clone https://github.com/thackl/perl5lib-Gff.git
git clone https://github.com/thackl/perl5lib-SVG-Bio.git

export PERL5LIB=/path/to/perl5lib-Gff/lib:/path/to/perl5lib-SVG-Bio/lib:$PERL5LIB;

bio2svg --fasta FA --region REGION --gff GFF --bam BAM > SVG
#+END_SRC

Region can be either a sequence ID (Chr4) or an ID with range (Chr4:521-15521).

***** Sample
#+BEGIN_SRC 

bio2svg --width 10000 --fa MaV-is-CrEc-001.ctg.fa --region MaV-is-CrEc-001 \
 --gff mav-regions.gff --gff MaV-gen-2.0.maker.lifted.gff \
 --gff CrEc-gen-dp-1.0.all.lifted.gff \
 --bam PCR\~MaV-is-CrEc-001.ctg.bam \
 --bam pr-all\~MaV-is-CrEc-001.ctg-support.bam \
 --bam pr-all~MaV-is-CrEc-001.ctg-bridge.bam \
 > MaV-is-CrEc-001.ctg.svg

#+END_SRC

[[etc/bio2svg-sample.png]]
[[etc/bio2svg-sample.svg]]