Use a file of gene queries to pull similar sequences from short-read nucleotide datasets, assemble gene contigs, reverse complement, and trim sequences based on blast results.
Functions:
- Pull gene sequences from datasets using a high throughput snakemake pipeline.
- CAP3 assembly of pulled sequences (useful for short-read sequences, not long-read).
- Autoreverse complements sequences based on blast results against the top gene queries.
- Trims sequence ends based on blast results against the top gene queries.
- note: the more robust your query sequences (taxonomy and size), the more robust trimming will be.
- Sequence size filter (default: <500bp sequences are removed).
- Sequences and output files are automatically named based on input file names and gene file names.
- Easy-to-parse directories and file names.
- Useful logs.
Use examples:
- Pull marker genes for organism identification (18S, 16S, COI).
- Find virus-related genes in organism transcriptomes.
Use the provided yaml file to create the seqpull environment
git clone https://github.com/SingleEukaryote/seqpull
cd seqpull/code
conda env create -f env/seqpull.yaml
- Put fasta files you want to pull sequences from in the data/DNAinputs directory. (must end with .fas or .fasta to be recognized)
- Put fasta files you want to use as gene queries in the data/gene_queries directory. (must end with .fas or .fasta to be recognized)
- Provided queries include 18S, 16S, and actin genes. Please curate your own queries depending on the target organisms and genes.
- Move to code directory.
- Do a dry run: snakemake -n
- Allows you to preview every step of the pipeline and every file being generated.
- Run bash script: bash seqpull.sh
- Modify cores/threads first
- Optionally, use in a queue system.
- From the terminal you can run:
- snakemake --cores 4 --keep-going > log.txt
