Common Files


The tarball includes source and pre-built binaries for a Linux-amd64 to run the Bambus 2 pipeline with CA. The pipeline requires AMOS 3.0.1 and CA 6.1. The Staphylococcus aureus assembly also requires Bowtie to be installed.

The rest of this guide assumes you have installed these tools and they are available in your path. For more information, please see the README.


Staphylococcus aureus


Here are the step-by-step instructions to reproduce this assembly:

  1. Step 1: Download tarball above and run tar xvzf gageBambusPackage.tar.gz
  2. Step 2: Download data below and run tar xvzf staph.tar.gz
  3. Step 3: Run cd bambus2
  4. Step 4: Run fastqToCA -insertsize 180 20 -libraryname frag -innie -type sanger -fastq `pwd`/frag_1.cor.fastq,`pwd`/frag_2.cor.fastq > frag_12.cor.frg
  5. Step 5: Run sh run.sh
  6. Step 6: Done!

Here are the files you will need:

  1. tarball of data + run scripts.
  2. sample output

Rhodobacter sphaeroides


Here are the step-by-step instructions to reproduce this assembly:

  1. Step 1: Download tarball above and run tar xvzf gageBambusPackage.tar.gz
  2. Step 2: Download data below and run tar xvzf rhodo.tar.gz
  3. Step 3: Run cd bambus2
  4. Step 4: Run fastqToCA -insertsize 180 20 -libraryname frag -innie -type sanger -fastq `pwd`/frag_1.cor.fastq,`pwd`/frag_2.cor.fastq > frag_12.cor.frg
  5. Step 5: Run fastqToCA -libraryname short -type sanger -fastq `pwd`/short_12.cor.ignore > short_12.cor.frg
  6. Step 6: Run sh run.sh
  7. Step 7: Done!

Here are the files you will need:

  1. tarball of data + run scripts.
  2. sample output

Human Chromosome 14


Here are the step-by-step instructions to reproduce this assembly:

  1. Step 1: Download tarball above and run tar xvzf gageBambusPackage.tar.gz
  2. Step 2: Download data below and run tar xvzf human.tar.gz
  3. Step 3: Run cd bambus2
  4. Step 4: Run fastqToCA -insertsize 180 20 -libraryname frag -innie -type sanger -fastq `pwd`/chr14_fragment_1.cor.fastq,`pwd`/chr14_fragment_2.cor.fastq > chr14_fragment_12.cor.fastq
  5. Step 5: Run fastqToCA -type sanger -libraryname lj -fastq `pwd`/chr14_longjump_12.cor.fastq > chr14_longjump_12.frg
  6. Step 6: Run fastqToCA -type sanger -libraryname sj -fastq `pwd`/chr14_shortjump_12.cor.fastq > chr14_shortjump_12.frg
  7. Step 7: Run sh run.sh
  8. Step 8: Done!

Here are the files you will need:

  1. tarball of data + run scripts.
  2. sample output