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Last pushed: 3 years ago
Short Description
Genome assembly using Nanopore-guided long and error-free DNA reads
Full Description

NaS is a hybrid approach developed to take advantage of data generated using MinION device. We combine Illumina and Oxford Nanopore technologies to produce NaS (Nanopore Synthetic-long) reads of up to 60 kb that aligned with no error to the reference genome and spanned repetitive regions.

NaS uses the MinION® read as a template to recruit Illumina reads and, by performing a local assembly, build a high-quality synthetic read. In the first step, a stringent alignment using BLAT (fast mode) or LAST (sensitive mode) is performed to retrieve Illumina short reads and their complementary sequences, called seed-reads. Next, the seed-read set is extended by searching for similar reads and their complementary sequences in the initial set using Compareads (two reads are considered similar if they share several common k-mers). This second step is crucial to retrieve Illumina reads that correspond to low-quality regions of the template. Finally, a microassembly of the reads is performed, instead of a classical polishing of the consensus, using an overlap-layout-consensus strategy, and repeats are resolved by a graph traversal algorithm.

NaS is distributed open-source under CeCILL FREE SOFTWARE LICENSE. Check out for more information about the contents of this license.

NaS home on the web is NaS website!

Visit NaS GitHub!

Contact : nas [a] genoscope [.] cns [.] fr

Due to legal restriction, we can’t provide Newbler binaries with NaS. You must download newbler archive from Roche website
Then, when you run NaS docker, you provide Newbler archive.

Run this container with :

sudo docker run -it -v $ABSOLUTE_PATH_TO_NEWBLER_ARCHIVE/DataAnalysis_2.9_All_20130530_1559.tgz:/home/bin/newbler.tgz -v $ABSOLUTE_PATH_TO_YOUR_READS:/home/Reads -c $NB_CPU -m $MEMORY rdbioseq/nas

For example, to test the program :

0) Download Newbler from Roche website :
1) Download this example dataset :


2) Untar/unzip the archive :

tar -zxvf NaS_example_acineto.tar.gz

3) Run:

sudo docker run -it -v $ABSOLUTE_PATH_TO_NEWBLER_ARCHIVE/DataAnalysis_2.9_All_20130530_1559.tgz:/home/bin/newbler.tgz -v $PWD/NaS_example_acineto:/home/Reads -c 5 -m 8g rdbioseq/nas

4) In the container run :

NaS --fq1 Reads/AWK_DOSF_1_1_A5KR6.IND3_clean.10prc.fastq --fq2 Reads/AWK_DOSF_1_2_A5KR6.IND3_clean.10prc.fastq --nano Reads/MinION_reads_Acinetobacter_baylyi.fa --out Reads/NaS_example_output --nb_proc 5

5) Quit the container with: exit

6) Retrieve your NaS reads in $PWD/NaS_example_acineto/NaS_example_output

See for more information about -c and -m option


run parallel --bibtex and write "will cite" to disable parallel annoying message

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