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antigen

bacon

BACoN stands for "Bait, Assemble and Compare Nanopore".

bacteria_genome_assembly

basecall_nanopore

basecall_nanopore_dorado

batchrenamer

Window app to batch rename files

bga

Bacterial Genome Assembly

bga_short

Bacterial Genome Assembly using short reads.

brucella_pcr

In silico Bruce-Ladder, Suis-Ladder and AMOS PCR

brucellaid

Brucella species identification using Illumina paired-end fastq.

companion

Companion computer startup scripts and examples

cowsnphr

SNV discovery pipeline

crispr_assay_tester

Test CRISPR assay specificity and sensitivity on small genomes

fast5_demultiplexer

Demultiplex fast5 reads based on Guppy output

fastq_editor

Prepend or append a specified sequence to all entries in fastq files in a folder

file_length_reporter

Windows tool to detect long absolute file paths that interfere with backups

filelengthreporter

Windows app to report the length of the files recursively from a specific path

fixstart

gbs_deepvariant

GBS pipeline for single-end or paired-end short reads (Illumina or IonTorrent).

gbs_stacks

A pipeline to process Genotyping-by-Sequencing (GBS) data from Illimina or IonTorrent using stacks to call the genotypes and variants.

gbsx

GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments

genome_comparator

Compare and visualize distances between genomes quickly

genome_filter

Filter downloaded genomes using BUSCO and QUAST

hybrid_assembly

Hybrid assembly pipeline for PacBio and Illumina paired-end data

in_silico_pcr

insilicopcr

installation

Instruction to install bioinformatic tools under Ubuntu

mashid

mcsc_decontamination

Scripts and documentations on the MCSC decontamination method

metagenomics