Pinned Repositories
OMArk
BRAKER
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
aneuploidy_detection
Script uses simply alignment and a hard threshold for deviation in order to detect changes in coverage
functional_enrichment
functional enrichment of starship cargo versus non-cargo and between isolates of different origins
Identifying_redundancy
Small script designed to take a single genome assembly and identify contigs which show redundancy with large contigs through BLAST alignment
MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
pggb_starship_pipeline
PhasedDiploidGenomeAssemblyPipeline
Using de-novo assembly and read-phasing to assemble reference-free diploid genomes
publicgenomes-to-buscophylogeny
Downloading sets of public genomes, analysing BUSCOs and generating trees for such genomes.
sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
SAMtoBAM's Repositories
SAMtoBAM/MUMandCo
MUM&Co is a simple bash script that uses Whole Genome Alignment information provided by MUMmer (only v4) to detect Structural Variation
SAMtoBAM/PhasedDiploidGenomeAssemblyPipeline
Using de-novo assembly and read-phasing to assemble reference-free diploid genomes
SAMtoBAM/aneuploidy_detection
Script uses simply alignment and a hard threshold for deviation in order to detect changes in coverage
SAMtoBAM/Identifying_redundancy
Small script designed to take a single genome assembly and identify contigs which show redundancy with large contigs through BLAST alignment
SAMtoBAM/pggb_starship_pipeline
SAMtoBAM/functional_enrichment
functional enrichment of starship cargo versus non-cargo and between isolates of different origins
SAMtoBAM/publicgenomes-to-buscophylogeny
Downloading sets of public genomes, analysing BUSCOs and generating trees for such genomes.