Splice aligner of long transcriptomic reads to genome.
Project description
uLTRA
uLTRA is a tool for splice alignment of long transcriptomic reads to a genome, guided by a database of exon annotations. uLTRA takes reads in fast(a/q) and a genome annotation as input and outputs a SAM-file. The SAM-file includes information on which splice sites are found and if the read is a full splice match (and to which transcript), incomplete splice match, Novel in catalog, or novel not in the catalog, as defined in SQANTI. uLTRA is highly accurate when aligning to small exons see some examples.
uLTRA is distributed as a python package supported on Linux / OSX with python v>=3.4. .
Table of Contents
INSTALLATION
Using conda
Conda is the preferred way to install uLTRA.
- Create and activate a new environment called ultra
conda create -n ultra python=3 pip
source activate ultra
- Install uLTRA
pip install ultra_bioinformatics
- You should now have 'uLTRA' installed; try it:
uLTRA --help
- Install slaMEM
git clone git@github.com:fjdf/slaMEM.git
cd slaMEM
make
And either place the generated binary slaMEM
in your path or run export PATH=$PATH:$PWD/
if you are in the slaMEM folder).
Upon start/login to your server/computer you need to activate the conda environment "ultra" to run uLTRA as:
source activate ultra
Downloading source from GitHub
Dependencies
Make sure the below-listed dependencies are installed (installation links below). Versions in parenthesis are suggested as uLTRA has not been tested with earlier versions of these libraries. However, uLTRA may also work with earlier versions of these libraries.
With these dependencies installed. Run
git clone https://github.com/ksahlin/uLTRA.git
cd uLTRA
./uLTRA
USAGE
uLTRA can be used with either Iso-Seq or ONT reads.
Indexing
First, we construct the data structures used in uLTRA using a genome annotation GTF file and a genome fasta file.
uLTRA prep_splicing all_genes.gtf outfolder/ [parameters]
uLTRA prep_seqs genome.fasta outfolder/ [parameters]
Aligning
For example, to align ONT cDNA reads using 48 cores, run
uLTRA align genome.fasta reads.[fa/fq] outfolder/ --ont --t 48 # ONT cDNA reads using 48 cores
uLTRA align genome.fasta reads.[fa/fq] outfolder/ --isoseq --t 48 # PacBio isoseq reads
uLTRA align genome.fasta reads.[fa/fq] outfolder/ --k 14 --t 48 # PacBio dRNA reads or reads with >10-12% error rate
Pipeline
Performs all the steps in one
uLTRA pipeline test/SIRV_genes_C_170612a.gtf test/SIRV_genes.fasta test/reads.fa outfolder/ [parameters]
Output
uLTRA outputs a SAM-file with alignments to the genome. In addition, it outputs to extra tags describing whether all the splices sites are known and annotated (FSM), new splice combinations (NIC), etc. For details see the definitions of notations in the Sqanti paper.
CREDITS
Please cite [1] when using uLTRA.
- Kristoffer Sahlin, Veli Makinen (2019) "Accurate spliced alignment of long RNA sequencing reads". (In preparation)
Bib record:
LICENCE
GPL v3.0, see LICENSE.txt.
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