wgharib/long-reads repository overview

⁠Software list

• Canu : https://github.com/marbl/canu⁠
• MHAP : https://github.com/marbl/MHAP⁠
• blasr : https://github.com/PacificBiosciences/blasr⁠
• R : https://www.r-project.org/⁠
• minimap2 : https://github.com/lh3/minimap2⁠
• miniasm : https://github.com/lh3/miniasm⁠
• quast : https://github.com/ablab/quast⁠

--- RNA part ---

• GMAP for alignment of RNA-seq reads to genome : research-pub.gene.com/gmap/
• poretools for MinION reads extraction: https://github.com/arq5x/poretools⁠
• pbh5tools to extract PB reads: https://github.com/PacificBiosciences/pbh5tools⁠
• matchAnnot.py` for PB transcriptome comparison to annotation: https://github.com/TomSkelly/MatchAnnot⁠
• cufflinks v2 + cuffcompare and gffread

⁠Usage with docker pull

⁠Connect as training

In a terminal run:

docker run -v <my/local/directory>:/home/training -p 8000:80 -p 9000:443 -d wgharib/long-reads

On your Browser :

• localhost:9000 Gate one --> click terminal ssh --> hit enter twice until you reach user: -->

user: training passwd: training

and

• localhost:8000 (apache web server mainly used to browse files)

⁠Connect as root:

docker run -it --workdir="/home/training" -v <my/local/directory>:/home/training wgharib/long-reads:latest /bin/bash

⁠Soft usage

⁠Canu

Usage : canu

⁠MHAP

Usage: java -jar /java/mhap-2.1.3.jar

⁠blasr:

First load this:

export PATH="/opt/pacbio/bin:$PATH"
export LD_LIBRARY_PATH="/opt/pacbio/lib::${LD_LIBRARY_PATH}"

usage: blasr, bax2bam (all executables pacbio are in /opt/pacbio/bin)

⁠R:

R

⁠minimap2:

usage: minimap2

⁠miniasm:

usage: miniasm

⁠quast

usage: quast.py

⁠--- RNA part ---

⁠GMAP

usage: gmap or gsnap

⁠poretools

usage: poretools

⁠pbh5tools

usage: bash5tools.py

⁠matchAnnot.py

usage: matchAnnot.py

⁠cufflinks

Usage : cufflinks incl. cuffcompare and gffread