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. It also assumed you have downloaded the tarball above and it is available under location </path/to/tarball>. For more information, please see the README. For original recipes (as published in Supplementary Materials) that include data in the distributions click here.


Staphylococcus aureus


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

  1. Download the original and Allpaths corrected data for Staphylococcus aureus.
  2. Run tar xvzf Data.original.tgz and tar xvzf Data.allpathsCor.tgz
  3. Download data below and run tar xvzf staph.tar.gz
  4. Run cd bambus2
  5. Run sh run.sh </path/to/tarball>/bin

Here are the files you will need:

  1. tarball of run scripts.
  2. sample output

Rhodobacter sphaeroides


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

  1. Download the Allpaths corrected data for Rhodobacter sphaeroides.
  2. Run tar xvzf Data.allpathsCor.tgz
  3. Download data below and run tar xvzf rhodo.tar.gz
  4. Run cd bambus2
  5. Run sh run.sh </path/to/tarball>/bin

Here are the files you will need:

  1. tarball of run scripts.
  2. sample output

Human Chromosome 14


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

  1. Download the Allpaths corrected data for Human Chromosome 14.
  2. Run tar xvzf Data.allpathsCor.tgz
  3. Download data below and run tar xvzf human.tar.gz
  4. Run cd bambus2
  5. Run sh run.sh </path/to/tarball>/bin

Here are the files you will need:

  1. tarball of run scripts.
  2. sample output