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Graham Larue's Projects

biogl icon biogl

A collection of (semi) useful small bioinformatics modules

cdseq icon cdseq

Extract coding sequence(s) from a genome and annotation file

climail icon climail

Send an email from the command-line

faseq icon faseq

Retrieves one or more sub-sequences from a FASTA file based on location, coordinate and strand information.

fasterq_dump icon fasterq_dump

A (faster) wrapper for NCBI's fastq-dump with some convenience functions

intronic icon intronic

Retrieve annotated intron sequences and classify them as minor (U12-type) or major (U2-type) using a support vector-machine model.

jgi-query icon jgi-query

A simple command-line tool to download data from Joint Genome Institute databases

minor_introns icon minor_introns

Plots and figures associated with https://doi.org/10.1093/nar/gkad797

notify icon notify

Send an email upon completion of a command-line command.

palign icon palign

Parallelized sequence alignment using BLAST or DIAMOND

randl icon randl

Retrieve random subsets of lines from a file

reciprologs icon reciprologs

Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.

revcomp icon revcomp

Reverse-complement a DNA/RNA sequence

tophits icon tophits

Get the specified number of top BLAST hits from a BLAST results file

transeq icon transeq

Translate nucleotide --> amino acid sequence

unifi-ddns icon unifi-ddns

Cloudflare DDNS (Dynamic DNS) support for UniFi OS

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