10 projects
primer-finder
Find group-specific kmers to design selective qPCR assays.
brucellaid
Identify the Brucella species of a read set with MASH, and type it with MLST
hashbrown-assembly
Long-read, short-read and hybrid bacterial genome assembly pipeline.
seqcounter
Count the occurrences of reference sequences in sequencing reads or genome assemblies
brucetyper
In silico Bruce-ladder, Suis-ladder, AMOS and RB51 junction PCR for Brucella
pycoqc-ng
Interactive QC metrics and plots for Oxford Nanopore sequencing data
nanotimesort
Bin Oxford Nanopore reads by cumulative sequencing time intervals (Guppy and Dorado compatible)
spoligotyper
In silico spoligotyping of Mycobacterium tuberculosis complex genomes from reads or assemblies
genome-comparator
Fast genome comparison with Mash: distance matrix, UPGMA/NJ/ME trees with bootstrap support, and interactive PCoA
qiime2-its
QIIME2 ITS metabarcoding pipeline for single-end (IonTorrent) and paired-end (Illumina) data
