Public Repository

Last pushed: a year ago
Short Description
PacBio smrtanalysis_2.3.0.140936 pre-built
Full Description

To use it

sudo docker run -it -v /home/bowhan/myData:/data bowhan/smrtanalysis-2.3.0.140936 bash
# -it option creates an interactive shell inside of the container
# -v option mount host directory to a directory inside of the container
# /home/bowhan/myData is where you store your data (i.e., h5 files)
# /data is the directory mounted inside the container

inside of docker

# invoke smrtshell, which prepares the enviroment for smrtanalysis
/opt/smrtanalysis/current/smrtcmds/bin/smrtshell
# run specific analysis; for example, to run iso-seq
# 1. generate CCS from h5 files, whose names are stored in a fofn (file of file names)
ConsensusTools.sh CircularConsensus  \
    --minFullPasses 0  --minPredictedAccuracy 75 \
    --parameters /opt/smrtanalysis/install/smrtanalysis_2.3.0.140936/analysis/etc/algorithm_parameters/2014-09/ \
    --numThreads 8 --fofn /data/input.fofn \
    -o /data/output

# 2. run Iso-Seq classify
pbtranscript.py classify \
    --cpus 8 --min_seq_len 300 \
    --flnc ${prefix}.isoseq_flnc.fasta \
    --nfl ${prefix}.isoseq_nfl.fasta \
    -d ${prefix}.out \
    ${prefix}.ccs.fa \
    ${prefix}.isoseq_draft.fasta 

# 3. run iso-seq cluster
pbtranscript.py cluster \
    isoseq_flnc.fasta final.consensus.fa \
    --nfl_fa isoseq_nfl.fasta -d clusterOut \
    --ccs_fofn reads_of_insert.fofn --bas_fofn input.fofn \
    --cDNA_size under1k --quiver --blasr_nproc 8 \
    --quiver_nproc 8
Docker Pull Command
Owner
bowhan

Comments (0)