TIPP: Telomere local assembly, Improved whole genome polish, and Plastid assembly
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This image packages a collection of 3 tools for Telomere local assembly, Improved whole genome polish, and Plastid assembly (TIPP).
The source code is available at (https://github.com/Wenfei-Xian/TIPP). A Dockerfile is included in the Github repository, if you prefer to build the image yourself.
# Pull the image from Dockerhub
docker pull weigelworld/tipp:latest
# Start an interactive shell in the container
docker run -it weigelworld/tipp:latest
Inside the container, the tools described below are directly accessible via command line. An example run of TIPP_plastid would work as follows:
(base) root@84037bc1f36c:~# cd
# Download an example dataset
wget -O Arabidopsis_thaliana.4X.fastq.gz https://figshare.com/ndownloader/files/47427487
# Run TIPP_plastid command
TIPP_plastid.v2.1.pl -f Arabidopsis_thaliana.4X.fastq.gz
The above example does not pass data to or from the host system -- please check the Docker documentation on how to exchange data between the host system and the container.
As an example, the following command would run an interactive shell in the container and mount the directory /data/experiments on the host system and make it available under /mnt inside the container:
docker run -it -v /data/experiments:/mnt weigelworld/tipp:latest
Apptainer, or formerly Singularity can be used to easily run TIPP when Docker is not available. If it is not installed on your system, it can be installed without super user rights, e.g. via conda from conda-forge.
The procedure to run TIPP via Singularity/Apptainer is similar to the above. Here, we show an example with apptainer, but the same parameters work with singularity.
# Pull the image from Dockerhub
apptainer pull docker://weigelworld/tipp:latest
# Start an interactive shell in the container
apptainer run tipp_latest.sif
Inside the container, the same example commands shown above can be run:
# Download an example dataset
wget -O Arabidopsis_thaliana.4X.fastq.gz https://figshare.com/ndownloader/files/47427487
# Run TIPP_plastid command
TIPP_plastid.v2.1.pl -f Arabidopsis_thaliana.4X.fastq.gz
By default, apptainer mounts your home and the current working directory inside the container. Thus, your data will be stored on the host file system. You can mount additional volumes as required (see Apptainer documentation ).
Usage: TIPP_plastid.v2.1.pl [options]
-h: Show this help message.
-f: HiFi reads (required).
-g: chloroplast or organelle (default: organelle).
-t: Threads for tiara, flye, KMC3 and readskmercount.
-n: Number of reads in each downsample for chloroplast.
-r: Number of random downsamplings (default: 5).
-p: Sequencing platform - either 'pacbio' or 'ont'. Only Q20 reads are accepted (default: pacbio).
-i: Assume the presence of the inverted repeats (default: 1).
-v: version.
Usage: TIPP_telomere.pl
-h: show this help message.
-u: telomere unit.
-f: hifi reads.
-e: extend the contigs with new assembled telomere sequences.(default=0, no extend)
-c: contigs. If the extension is not specified, it will be used as the output name.
-t: threads for minimap2.
-m: minimum length of uniq sequence (without telomere)
Content type
Image
Digest
sha256:6dea3887c…
Size
2.8 GB
Last updated
almost 2 years ago
docker pull weigelworld/tipp