Hague

An adjacency-list based De Bruijn graphs implementation

Build requirements

C compiler
make
zlib
gengetopt

Tested on Ubuntu 16.04 and Windows 10 using Ubuntu bash

Build

Download from Github

$ git clone git git@github.com:ericniso/hague.git
$ cd hague

Download submodules

$ git submodule init
$ git submodule update

Compile binaries, executable file is in debug folder

$ make bin

Compile debug binaries, executable file is in debug folder

$ make debug

Compile shared library, lib file is in lib folder

$ make lib

Compile all previous targets

$ make all

Test

After compiling the source code, we recommend to run automated tests in order to check for compilation success

$ make test

Documentation

Docs can be generated using

$ make doc

This will generated source code documentation both in html and latex in docs folder

Usage

$ hague -f "/path/to/fasta/file" -k "k-mer-length"

Input file can be compressed .gz or not

Such command will generate the de Bruijn graph and output the result in csv format, here is an example output:

$ hague -f ~/home/nicolaas/chr1_KI270707v1_random.fa.gz -k 10 | head -n 5
Source, Target, Label
AGGGGTCTG, GGGGTCTGC, AGGGGTCTGC
GGGGTCTGC, GGGTCTGCT, GGGGTCTGCT
GGGTCTGCT, GGTCTGCTT, GGGTCTGCTT
GGTCTGCTT, GTCTGCTTA, GGTCTGCTTA

From left to right we can see:

Source is the source node, whose key is a (k-1)-mer
Target is the node that the source node is pointing to through and edge
Label is the edge label connecting the previous two nodes, and represents the corresponding k-mer string

If you want to redirect the output to a file you can specify a filename using the -o option:

$ hague -f "/path/to/fasta/file" -k "k-mer-length" -o "/path/to/output/file"

There’s an additional feature, which is the superstring reconstruction, invoked by adding -w option:

$ hague -f "/path/to/fasta/file" -k "k-mer-length" -w [-o "/path/to/output/file"]

Currently this is only a work in progress, since it only works if the graph is Eulerian (semi-Eulerian)

Authors

Eric Nisoli, Lorenzo Mammana

License

MIT LICENSE