I just finished up throwing together some useful commands for working with Illumina sequencing data and thought it could be useful for others as well!
Nucleotide_Essentials.jl is a collection of tools for working with Illumina next-generation sequencing reads currently under development and testing.
Installation:
Active development is still underway but the most current version can be downloaded from the REPL using:
The package is registered in the General registry and so can be installed at the REPL with:
] add Nucleotide_Essentials
Current Functions:
-
readFastq- Import a .fastq file into Julia -
readFasta- Import a .fasta file into Julia -
writeFasta- Write a .fasta or .fasta.gz to file -
FilterQuality_se- Filter single-ended Illumina reads -
FilterQuality_pe- Filter paired-end Illumina reads -
FastqtoFasta- Convert a .fastq file or FastqRecord to a FastaRecord -
potential_mismatches- Create a list of potential mismatch barcodes (mutations + deletions) -
demultiplex_se- Demultiplex single-end Illumina reads -
demultiplex_pe- Demultiplex paired-end Illumina reads -
PlotQuality- Visualize quality of .fastq file
For bug fixes, new features, and future suggestions, open an issue!
Full documentation can be found at here