capsim

Capsim is a tool to simulate capture sequencing. It was developed as part of the Japsa package.

Quick installation guide:

On a Linux/Mac machine with make' andgit' installed, the software can be installed with

git clone https://github.com/mdcao/japsa
cd japsa
make install \
  [INSTALL_DIR=~/.usr/local \] 
  [MXMEM=7000m \] 
  [SERVER=true \]

Details of installation (including for Windows) and usage of Japsa can be found in its documentation hosted on ReadTheDocs

Usage

Before running capsim, the probe sequences need to be aligned to the reference sequence (or the genome sequence to simulate sequencing). We recommend using bowtie2 for the alignment.

#Skip this step if the index has been generated
bowtie2-build ref.fasta ref

#Align the probes into the reference
bowtie2 --local --very-sensitive-local --mp 8 --rdg 10,8 --rfg 10,8 -k 10000 -f -x ref -U probes.fa -S probes.sam

Note: for some reason, bowtie2 only accepts the query fasta file (probes.fa) containing one sequence per line.

After alignment, sort the and index the bam file with samtools

 samtools view -bSU probes.sam | samtools sort -o probes.bam -

Capsim takes the bam file as the input:

jsa.sim.capsim --reference ref.fasta --probe probes.bam --ID someid --fmedian 5000  --pacbio output --pblen 3000 --num 20000000

or

jsa.sim.capsim --reference ref.fasta --probe probes.bam --ID someid --fmedian 500  --miseq output --illen 300 --num 20000000