ABruijn is a assembler for long reads from, for example, PacBio and Oxford Nanopore Technologies sequencers. It uses an A-Bruijn graph to find the overlaps between reads without error correction. It then produces a draft assembly from a subset of raw reads which is then polished into a high quality assembly using all reads. A 5Mb bacterial genome with ~80x coverage was be assembled on one of our compute nodes (10GB memory; 16 CPUs) in about 30min. A 150 Mb D. melanogaster genome was assembled in 2 days (520GB memory; 32 CPUs).
There may be multiple versions of abruijn available. An easy way of selecting the version is to use modules. To see the modules available, type
module avail abruijn
To select a module use
module load abruijn/[version]
where [version] is the version of choice.
abruijn is a multithreaded application. Make sure to match the number of cpus requested with the number of threads.
Environment variables set
-
$PATH -
$ABRUIJN_TEST_DATA
Dependencies
- singularity
Loaded automatically.
References
- Yu Lina, Jeffrey Yuana, Mikhail Kolmogorova, Max W. Shena, Mark Chaissonb, and Pavel A. Pevzner. Assembly of long error-prone reads using de Bruijn graphs PNAS 2016, 27:E8396-E8405 PubMed | PMC | Journal
The test data was obtained from Kim et al..
Documentation
Allocate an interactive session with sinteractive and use as described below
biowulf$ sinteractive --mem=5g --cpus-per-task=16 --gres=lscratch:10
node$ module load abruijn
node$ cd /lscratch/$SLURM_JOB_ID
node$ zcat $ABRUIJN_TEST_DATA/SRR1284073_gt10k.fasta.gz > SRR1284073_gt10k.fasta
node$ abruijn -t $SLURM_CPUS_PER_TASK -p pacbio \
SRR1284073_gt10k.fasta assembly_ecoli 80
[21:03:38] INFO: Running ABruijn
[21:03:38] INFO: Assembling reads
[21:03:49] INFO: Counting kmers (1/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:04:40] INFO: Counting kmers (2/2):
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:04:54] INFO: Building kmer index
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:05:23] INFO: Finding overlaps:
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:07:07] INFO: Extending reads
[21:07:10] INFO: Assembled 1 contigs
[21:07:10] INFO: Generating contig sequences
[21:07:39] INFO: Polishing genome (1/2)
[21:07:39] INFO: Running BLASR
[21:10:53] INFO: Separating draft genome into bubbles
[21:14:51] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:27:29] INFO: Polishing genome (2/2)
[21:27:29] INFO: Running BLASR
[21:29:46] INFO: Separating draft genome into bubbles
[21:33:58] INFO: Correcting bubbles
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
[21:39:15] INFO: Done! Your assembly is in file: /lscratch/12345/assembly_ecoli
node$ ll assembly_ecoli
total 2.3G
-rw-rw-r-- 1 user group 1.1M Jan 10 21:39 abruijn.log
-rw-rw-r-- 1 user group 42 Jan 10 21:39 abruijn.save
-rw-rw-r-- 1 user group 798M Jan 10 21:10 blasr_1.m5
-rw-rw-r-- 1 user group 839M Jan 10 21:29 blasr_2.m5
-rw-rw-r-- 1 user group 268M Jan 10 21:14 bubbles_1.fasta
-rw-rw-r-- 1 user group 316M Jan 10 21:34 bubbles_2.fasta
-rw-rw-r-- 1 user group 7.2M Jan 10 21:27 consensus_1.fasta
-rw-rw-r-- 1 user group 13M Jan 10 21:39 consensus_2.fasta
-rw-rw-r-- 1 user group 4.8M Jan 10 21:07 draft_assembly.fasta
-rw-rw-r-- 1 user group 4.6M Jan 10 21:27 polished_1.fasta
-rw-rw-r-- 1 user group 4.6M Jan 10 21:39 polished_2.fasta
-rw-rw-r-- 1 user group 4.9M Jan 10 21:07 reads_order.fasta
node$ cp -r assembly_ecoli /data/user/badbadproject
node$ exit
biowulf$
Create a batch script similar to the following example:
#! /bin/bash
# this file is abruijn.batch
ml abruijn || exit 1
cd /lscratch/$SLURM_JOB_ID
cp /data/users/some/where/reads.fa .
abruijn -t $SLURM_CPUS_PER_TASK -p pacbio -k17 \
reads.fa assembly_dmelanogaster 90
cp -r assembly_dmelanogaster /data/user/badbadproject
This particular example made use of data set SRX499318 filtered to reads >14k length resulting in a 90x coverage of the ~150Mb D. melanogaster genome.
Submit to the queue with sbatch requesting sufficient memory and local scratch space:
biowulf$ sbatch --mem=600g --cpus-per-task=32 --partition=largemem --gres=lscratch:300 abruijn.batch
This job ran for ~2 days and used up to 520GB of memory. Here is the profile of memory and running threads for this assembly:
The final result was an assembly of 146.7Mb with 170 contigs and N50 = 5.33Mb.
