Daniel Bogema's repositories
mgt_scripts
Scripts to help in MGT scheme generation
gas
Basic annotation statistics for eukaryotic genomes
trycycler_scripts
Scripts for genome assembly with trycycler
genagr
Gene name grabber, grab fasta sequences from an annotated reference using gene names
CCMetagen
Microbiome classification pipeline
bohra
A pipeline for bioinformatics analysis of bacterial genomes
cervus_parse
A script for parsing zipped vcf files (from an Ion Torrent run) to a genotype format for Cervus
rucs_analysis
Collection of scripts for filtering and parse output from the RUCS pipeline
funannotate
Eukaryotic Genome Annotation Pipeline
T_ori_genome_pipeline
Theileria varaint calling pipeline
maker_genome_annotation
Collection of python scripts for genome annotation with maker
nullarbor_it
:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
marker_gene_phylogeny
Runs phylosift to generate a marker gene phylogeny, useful for intra-genus comparisons.
snp_phylogeny
A pipeline for running SNP-based phylogenetic analysis
bioconda-recipes
Conda recipes for the bioconda channel.
analysis_template
Starting point for a conda-based analysis folder
bact_vcp
Another variant calling pipeline