HINGE

A genome assembler attempting to assemble all that can be assembled but nothing more

© 2017. All rights reserved.

HINGE Quick Start

Installation

Dependencies

The following python packages are necessary:

This software is still at prototype stage so it is not well packaged, however it is designed in a modular flavor so different combinations of methods can be tested.

Installing the software is very easy.


git clone https://github.com/HingeAssembler/HINGE.git

cd HINGE

git submodule init

git submodule update

./utils/build.sh

Running

In order to call the programs from anywhere, I suggest one export the directory of binary file to system environment, you can do that by using the script setup.sh. The parameters are initialised in utils/nominal.ini. The path to nominal.ini has to be specified to run the scripts.

A demo run for assembling the ecoli genome is the following:

# Setup paths
source utils/setup.sh

# Setup destination directory
mkdir data/ecoli
cd data/ecoli
# reads.fasta should be in data/ecoli

# Run DAligner to get alignments
fasta2DB ecoli reads.fasta
DBsplit -x500 -s100 ecoli     
HPC.daligner -t5 ecoli | csh -v
# alternatively, you can put output of HPC.daligner to a bash file and edit it to support parallelisation


rm ecoli.*.ecoli.*
LAmerge ecoli.las ecoli.+([[:digit:]]).las
rm ecoli.*.las # we only need ecoli.las
DASqv -c100 ecoli ecoli.las

# Run filter

mkdir log

hinge filter --db ecoli --las \
ecoli.las -x ecoli --config <path-to-nominal.ini>

# Get maximal reads

hinge maximal --db ecoli --las \
ecoli.las -x ecoli --config <path-to-nominal.ini>

# Run layout

hinge layout --db ecoli --las ecoli.las \
 -x ecoli --config <path-to-nominal.ini> -o ecoli

# Run postprocessing

hinge clip ecoli.edges.hinges \
ecoli.hinge.list <identifier-of-run>


# get draft assembly

hinge draft-path <working directory> \
ecoli ecoli<identifier-of-run>.G2.graphml

hinge draft --db ecoli --las ecoli.las --prefix ecoli \
--config <path-to-nominal.ini> --out ecoli.draft


# get consensus assembly

hinge correct-head ecoli.draft.fasta \
 ecoli.draft.pb.fasta draft_map.txt

fasta2DB draft ecoli.draft.pb.fasta

HPC.daligner ecoli draft | zsh -v  

hinge consensus draft ecoli draft.ecoli.las \
ecoli.consensus.fasta <path-to-nominal.ini>

hinge gfa <working directory> \
 ecoli ecoli.consensus.fasta

#results should be in ecoli_consensus.gfa

Parameters

In the pipeline described above, several programs load their parameters from a configuration file in the ini format. All tunable parameters are described in this document.

Analysis of Results

showing ground truth on graph

Some programs are for debugging and oberservation. For example, one can get the ground truth by mapping reads to reference and get ecoli.ecoli.ref.las.

This las file can be parsed to json file for other programs to use.

run_mapping.py ecoli ecoli.ref ecoli.ecoli.ref.las 1-$

In the prune step, if ecoli.mapping.json exists, the output graphml file will contain the information of ground truth.

drawing alignment graphs and mapping graphs

Draw a read, for example 60947, and output figure to sample folder (need plus 1 as LAshow counts from 1):

draw2.py ecoli ecoli.las 60948 sample 100

Draw pileup on draft assembly, given a region represented as [start,end], which is [3600000, 4500000] in this case.

draw2_pileup_region.py  3600000 4500000