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Last pushed: 2 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 http://www.cecill.info/ 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 http://www.454.com/products/analysis-software/
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 : http://www.454.com/products/analysis-software/
1) Download this example dataset :

wget http://www.genoscope.cns.fr/externe/nas/datasets/NaS_example_acineto.tar.gz

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 https://goldmann.pl/blog/2014/09/11/resource-management-in-docker/ for more information about -c and -m option

Optional

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

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rdbioseq

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