duceppemo Goto Github PK

nanopore_variant_calling_pepper

nanoqc

Quality control of Oxford Nanopore Technologies sequencing data from basecalled fastq files

nanotimesort

ncbi

Compilation of scrips related to stuff to do on NCBI

path_finder

List absolute paths recursively in DOS terminal

phame

Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to construct a phylogenetic tree. Provides evolutionary analyses (genes under positive selection) using CDS SNPs.

pilon_polish

Polish assembly (fasta) with Illumina paired-end reads (fastq)

pycoqc

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)

qiime2_its

QIIME2 pipeline for IonTorrent sequencing data

roary

Rapid large-scale prokaryote pan genome analysis

salmonella_snp_typing

salmonelle_snp_pcr

seedid

selective_primer_finder

Finds candidate kmers with high variability between an inclusion and an exclusion group to design qPCR assays.

seqcounter

smart_garden

Arduino project to automate plant watering and gather other environment data

snp_analysis

USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.

species_identification

spoligotyper

In silico spoligotyper for Mycobacterium bovis.

treerenamer

Windows App to Rename Phylogenetic Tree

vcfs_to_snp_alignment

USDA APHIS Veterinary Services (VS) Mycobacterium tuberculosis complex, mainly M. bovis, and Brucella sp. genotyping from whole genome sequence (WGS) outputting BAM, VCF, SNP tables and phylogentic trees.

vsnp3

vSNP -- validate SNPs