NanoFG

NanoFG integrates existing genomic tools and additonal code to provide an easy-to-use pipeline for the detection of fusion genes from Nanopore sequencing data

INSTALL

git clone https://github.com/SdeBlank/NanoFG.git NanoFG
cd NanoFG

virtualenv venv -p python3
. venv/bin/activate
pip install -r requirements.txt

Adjust all paths in the paths.ini file to installed tools

How to run

bash NanoFG.sh -f </path/to/fastqdir> [-n SAMPLE_NAME ] [-s SELECTION] [-cf] [-cc] [-df] [-dc]

OR

bash NanoFG.sh -b </path/to/bam> [-v </path/to/vcf>] [-n SAMPLE_NAME ] [-s SELECTION] [-cf] [-cc] [-df] [-dc]

For more information, see the wiki:
https://github.com/SdeBlank/NanoFG/wiki

Citation

Please see and cite: https://www.nature.com/articles/s41467-020-16641-7

Additionally, NanoFG integrates different existing tools:

Samtools (1.7) - http://samtools.sourceforge.net/

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Minimap2 (2.6) - https://github.com/lh3/minimap2

Li, H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100.

LAST (921) - http://last.cbrc.jp/doc/last.html

Kielbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Research 21, 487–493 (2011).

NanoSV (1.2.4) - https://github.com/mroosmalen/nanosv

Cretu Stancu, M. et al. Mapping and phasing of structural variation in patient genomes using nanopore sequencing. Nat. Commun. 8, 1326 (2017).

Wtdbg2 (2.2) - https://github.com/ruanjue/wtdbg2

Ruan, J. and Li, H. (2019) Fast and accurate long-read assembly with wtdbg2. Nat Methods

Primer3 - https://github.com/primer3-org/primer3

Untergasser, A. et al. Primer3–new capabilities and interfaces. Nucleic Acids Res. 40, e115 (2012).