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Last pushed: 7 months ago
Short Description
Docker image for Pipelign: an alignment pipeline for virus sequences
Full Description

Pipelign

Semi-automated computational pipeline for aligning virus sequences.

Pipelign can be downloade from github using the following command:

git clone https://github.com/asmmhossain/pipelign

Typing python3 Pipelign.py -h will give a short usage information

Dependencies:

  • Python 3
  • BioPython: for sequence processing
  • CD-HIT: for clustering 'long' sequences
  • IQ-TREE: for generating a phylogenetic tree of representative 'long' sequences
  • MAFFT: for alignment
  • HMMER: for matching sequence fragments to clusters
  • BLAST: for matching sequence fragments to clusters

Docker

Docker repository for Pipelign is hosted on asmmhossain/Pipelign. Anyone having Docker installed can get Pipelign using the command:

docker pull asmmhossain/pipelign

The following command will show the usage information and command line argument options for running Pipelign using docker:

docker run --rm asmmhossain/pipelign Pipelign.py -h

Then Pipelign can be run to produce alignments using desired options:

docker run -i -t --rm -v $(pwd):/data -w /data asmmhossain/pipelign Pipelign.py [options]

Please make sure the sequence file resides in the current directory from where the docker container is launched. Output file will be stored in the current directory.

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Owner
asmmhossain
Source Repository

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