BATISCAF - BAd conTIg removal SCAFfolding

General information

BATISCAF is a novel repeat aware scaffolding tool.

The main steps of the algorithms are:

1. Removal of "bad" contigs, i.e. contigs which are short and which are deemed to be repeated.
2. Solving the trivial scaffolding problem on the set of reliable contigs
3. Re-inserting the previously removed contigs into the scaffolds

Software prerequisites

Before running BATISCAF make sure that the following software is installed on your Linux computer:

• A short read aligner: Bowtie, Bowtie2, BWA, or another one
• IBM ILOG CPLEX >=12.7 - optimizer (solving Integer Linear Programs and many other stuff)
• Python 2.7 with the following libraries:
  • NetworkX >=2.0
  • Biopython

Running BATISCAF

• First, get BATISCAF from GitHub by executing the following command:

git clone https://github.com/mandricigor/batiscaf.git

and change the local directory:

cd batiscaf

• Next, prepare alignment files in .SAM format for the paired-end reads. We recommend using Bowtie2:

bowtie2-build -q -f $CONTIG_FILE $INDEX_FILE
bowtie2 --quiet --no-hd --reorder -k 10 -q -p 10 -x $INDEX_FILE -U $READ1_FASTQ -S $SAM1_FILE
bowtie2 --quiet --no-hd --reorder -k 10 -q -p 10 -x $INDEX_FILE -U $READ2_FASTQ -S $SAM2_FILE

• Obtain the scaffolding graph in .graphml format:

python scaffolding_graph.py -o OUTPUT_GRAPHML -c CONTIGS_FASTA -m1 MAPPINGS1 -m2 MAPPINGS2 -i INS_SIZE -p PAIR_MODE -s STD_DEV

• Run BATISCAF:

batiscaf.py --graphml SCAFFOLDING_GRAPH --fasta FASTA

By default, the scaffolds will be written to the file output.scaffolds.batiscaf.fasta.

Help

• In order to get more help for the scaffolding_graph.py helper script, execute the command:

python scaffolding_graph.py -h

You should see the following output:

usage: scaffolding_graph.py [-h] [-o OUTPUT_GRAPHML] [-c CONTIGS_FASTA] -m1
                          MAPPINGS1 -m2 MAPPINGS2 -i INS_SIZE -p PAIR_MODE
                          -s STD_DEV

BATISCAF scaffolding graph construction helper script. Produces a .graphml
file

optional arguments:
-h, --help         show this help message and exit
-o OUTPUT_GRAPHML  output graphml file
-c CONTIGS_FASTA   fasta file with contigs
-m1 MAPPINGS1      comma separated list of .sam files (first read in the
                   read pair)
-m2 MAPPINGS2      comma separated list of .sam files (second read in the
                   read pair)
-i INS_SIZE        insert sizes (comma separated values)
-p PAIR_MODE       pair modes (fr - innie style -> <-, rf - outtie style <-
                   ->) (comma separated values)
-s STD_DEV         libraries standard deviations (comma separated values)

• In order to get more help for the batiscaf.py main script, execute the command:

python batiscaf.py -h

You should see the following output:

usage: batiscaf.py [-h] --graphml SCAFFOLDING_GRAPH [--fasta FASTA]
                 [--filter_threshold FILTER_THRESHOLD] [--mst]

BATISCAF - BAd conTIg removal SCAFfolder.

optional arguments:
-h, --help            show this help message and exit
--fasta FASTA         output fasta file (default
                      output.scaffolds.batiscaf.fasta
--filter_threshold FILTER_THRESHOLD
                      filter out edges with weight less than this value
                      (default 5)
--mst                 find MST (minimum spanning tree) before running
                      BATISCAF algorithm

required arguments:
--graphml SCAFFOLDING_GRAPH
                      scaffolding graph in graphml format

Contact us

In order to get more information on BATISCAF, do not hesitate to contact Igor Mandric (Georgia State University).