LGAflow

LGAflow - A genome annotation pipeline for eukaryotes

LGAflow stands for Labtorary Genome Annotation workflow which is based on Nextflow framework.

NOTE: LGAflow is still under development, there might be some bugs during running

• LGAflow
  • Quick Start
    • Install Nextflow
    • Install Miniconda
    • Run Test
  • Usage
    • profile
    • inputs
    • databases
    • computing options
  • Citations

Quick Start

LGAflow is written in Nextflow and can be used in any Linux distribution. LGAflow uses conda or Linux Container (eg. Docker, Singularity) to manage dependencies. Nextflow and either conda, Docker, Singuilarity need to be installed before running the pipeline.

Install Nextflow

1. Typical installation

   # Make sure that Java v8+ is installed:
   java -version
   
   # Install Nextflow
   curl -fsSL get.nextflow.io | bash
   
   # Add Nextflow binary to your user's PATH:
   # mv nextflow ~/bin/
   
   # OR system-wide installation:
   # sudo mv nextflow /usr/local/bin

2. Using Bioconda

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   
   conda install nextflow

3. Using pre-built binaiers

   # Make sure that Java v8+ is installed:
   java -version
   
   # Get the executable from https://github.com/nextflow-io/nextflow/releases eg :
   wget https://github.com/nextflow-io/nextflow/releases/download/v21.10.6/nextflow-21.10.6-all -O nextflow
   
   # Add Nextflow binary to your user's PATH:
   # mv nextflow ~/bin/
   
   # OR system-wide installation:
   # sudo mv nextflow /usr/local/bin

Install Miniconda

Run Test

Test data can be obtained from http://seafile.itslab.lzu.edu.cn/f/f886da69fd4b4aafad65/

Usage

eg:

nextflow run dakehero/lgaflow -profile local,conda --cores 8 --memory 16.GB --genome ./test/c_elegans.fa --proteins ./test/proteins/ --reads ./test/RNA_Seq/ --species c_elegans --rm_species Caenorhabditis --augustus_species caenorhabditis --busco_db ./database/nematoda_odb10/ 

The above command shows how to perform genome annotation pipeline for Caenorhabditis elegans with LGAflow, several options should be specified.

profile

• data
  • test: using test data to run test annotation.
• executer(choose one)
  • local: use local executer to run the pipeline on a single-node computer.
  • slurm: use slurm executer to run the pipeline on a HPC cluster.
  • pbs: use torque executer to run the pipeline on a HPC cluster.
• environment engine(choose one)
  • conda
  • docker
  • singularity

inputs

• genome: genome assemably file in fasta format(eg: species.fa)
• reads: path of RNA-Seq fastq files (eg: /path/of/reads/)
• proteins: path of proteins file in fasta format(eg: /path/to/proteins)

databases

• busco_db: path of OrthoDB for the specie

computing options

• cores: max CPU cores per process
• memory: max memory per process
• queueSizemax queue size for batch scheduler
• useMamba using mamba instead of conda to create conda-env

Citations

• [1]“The UniVec Database.” https://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/ (accessed Dec. 16, 2021).
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• [4]M. Stanke and S. Waack, “Gene prediction with a hidden Markov model and a new intron submodel,” Bioinformatics, vol. 19 Suppl 2, pp. ii215-225, Oct. 2003, doi: 10.1093/bioinformatics/btg1080.
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• [6]F. A. Simão, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, “BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs,” Bioinformatics, vol. 31, no. 19, pp. 3210–3212, Oct. 2015, doi: 10.1093/bioinformatics/btv351.
• [7]W. Shen, S. Le, Y. Li, and F. Hu, “SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation,” PLOS ONE, vol. 11, no. 10, p. e0163962, Oct. 2016, doi: 10.1371/journal.pone.0163962.
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• [9]C. L. Schoch et al., “NCBI Taxonomy: a comprehensive update on curation, resources and tools,” Database, vol. 2020, p. baaa062, Jan. 2020, doi: 10.1093/database/baaa062.
• [10]A. R. Quinlan and I. M. Hall, “BEDTools: a flexible suite of utilities for comparing genomic features,” Bioinformatics, vol. 26, no. 6, pp. 841–842, Mar. 2010, doi: 10.1093/bioinformatics/btq033.
• [11]W. H. Majoros, M. Pertea, and S. L. Salzberg, “TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders,” Bioinformatics, vol. 20, no. 16, pp. 2878–2879, Nov. 2004, doi: 10.1093/bioinformatics/bth315.
• [12]M. Lataretu and M. Hölzer, “RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow,” Genes, vol. 11, no. 12, p. 1487, Dec. 2020, doi: 10.3390/genes11121487.
• [13]D. Kim, J. M. Paggi, C. Park, C. Bennett, and S. L. Salzberg, “Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype,” Nat Biotechnol, vol. 37, no. 8, pp. 907–915, Aug. 2019, doi: 10.1038/s41587-019-0201-4.
• [14]K. J. Hoff and M. Stanke, “Predicting Genes in Single Genomes with AUGUSTUS,” Current Protocols in Bioinformatics, vol. 65, no. 1, p. e57, 2019, doi: 10.1002/cpbi.57.
• [15]B. J. Haas et al., “Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments,” Genome Biology, vol. 9, no. 1, p. R7, Jan. 2008, doi: 10.1186/gb-2008-9-1-r7.
• [16]M. G. Grabherr et al., “Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data,” Nat Biotechnol, vol. 29, no. 7, pp. 644–652, May 2011, doi: 10.1038/nbt.1883.
• [17]S. Chen, Y. Zhou, Y. Chen, and J. Gu, “fastp: an ultra-fast all-in-one FASTQ preprocessor,” Bioinformatics, vol. 34, no. 17, pp. i884–i890, Sep. 2018, doi: 10.1093/bioinformatics/bty560.
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