Name: paladin
Owner: Fred Hutchinson Cancer Research Center
Description: Protein Alignment and Detection Interface
Forked from: twestbrookunh/paladin
Created: 2017-10-30 17:59:04.0
Updated: 2017-10-30 17:59:06.0
Pushed: 2017-11-07 17:22:26.0
Homepage: null
Size: 17694
Language: C
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Protein ALignment And Detection INterface
PALADIN is a protein sequence alignment tool designed for the accurate functional characterization of metagenomes.
PALADIN is based on BWA, and aligns sequences via read-mapping using BWT. PALADIN, however, offers the novel approach of aligning in the protein space. During the index phase, it processes the reference genome's nucleotide sequences and GTF/GFF annotation containing CDS entries, first converting these transcripts into the corresponding protein sequences, then creating the BWT and suffix array from these proteins. The process of translatation is skiped when providing a protein reference file (e.g., UniProt) for mapping. During the alignment phase, it attempts to find ORFs in the read sequences, then converts these to protein sequences, and aligns to the reference protein sequences.
PALADIN currently only supports single-end reads (or reads merged with FLASH, PEAR, abyss-mergepairs), and BWA-MEM based alignment. It makes use of many BWA parameters and is therefore compatible with many of its command line arguments.
PALADIN may output a standard SAM file, or a text file containing a UniProt-generated functional profile. This text file may be used for all downstream characterizations.
Dependencies
build-essential libcurl4-openssl-dev git make gcc zlib1g-dev. This should be available on Ubuntu 14.04 using sudo apt-get install build-essential libcurl4-openssl-dev git make gcc zlib1g-devclone https://github.com/twestbrookunh/paladin.git
aladin/
=$PATH:$(pwd)
Docker
Alternatively, you can use Paladin with the Docker image hosted at https://quay.io/repository/fhcrc-microbiome/paladin. This image can be downloaded with the command docker pull quay.io/fhcrc-microbiome/paladin. A set of tags are used to pin releases, e.g. v1.4.0--1 is the image pinned to the v1.4.0 version of Paladin.
Download and prepare UniProt Swiss-Prot index files.
din prepare -r1
Download and prepare UniProt UniRef90 index files.
din prepare -r2
Index UniProt (or another protein) fasta, if not using the automated prepare command
din index -r3 uniprot_sprot.fasta.gz
Align a set of reads using 4 theads. Send the full UniProt report to paladin_uniprot.tsv.
din align -t 4 -o paladin index input.fastq.gz
Align a set of reads using 4 theads. Produce a bam file.
din align -t 4 index input.fastq.gz | samtools view -Sb - > test.bam
Align a set of reads, preferring higher quality mappings over number of proteins detected.
din align -T 20 -o paladin index input.fastq.gz
Align a set of reads, report secondary alignments, and generate UniProt report for both primary and secondary alignments.
din align -a -o paladin index input.fastq.gz
If you're intersted in trying this out on a smallish test file, try downloading this one which is from a human lung metagenome study: http://www.ebi.ac.uk/ena/data/view/PRJNA71831
tall PALADIN as per above
-O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR117/002/SRR1177122/SRR1177122.fastq.gz
din prepare -r1 #unless already done
din align -t 4 -o lungstudy uniprot_sprot.fasta.gz SRR1177122.fastq.gz
k at report file, SAM, etc.
Wrapper script
This repo also contains a wrapper script (run.py) which is intended to make it easier to deploy Paladin on cloud or HPC computing resources (e.g. Slurm or AWS). The script is located in the PATH in the Docker image, and so you can run run.py -h to see the set of options for this script. In brief, users can specify the input URL, reference database path, and output folder location (any of which may be local paths, S3 buckets, or FTP). The run script will fetch the input data, run Paladin, wrap up the results into a single JSON output file, and copy the results to the specified output folder.
MAT
t Abundance Quality (Avg) Quality (Max) UniProtKB ID Organism Protein Names Genes Pathway Features Gene Ontology Reviewd Existence Comments Cross Reference (KEGG) Cross Reference (GeneID) Cross Reference (PATRIC) Cross Reference(EnsemblBacteria)
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