stollec's starred repositories
JupiterPlot
A Circos-based tool to visualize genome assembly consistency or synteny between assemblies.
exonerate-gff3
exonerate fork with added gff3 support
genomics_general
General tools for genomic analyses.
dnaPipeTE
dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
sequencetools
Set of scripts etc. to work with DNA sequence and related files
BNG-FragileSiteRepair
Scripts for repairing (stitching) fragile sites of BioNano genome maps.
sam2pairwise
sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.
quickmerge
A simple and fast metassembler and assembly gap filler designed for long molecule based assemblies.
OrthoFinder
Phylogenetic orthology inference for comparative genomics
ghost-tree
creating hybrid-gene phylogenetic trees for diversity analyses
newick_utils
shell tools for processing phylogenetic trees
dendroscope3
Dendroscope program for analyzing and visualizing rooted phylogenetic trees and networks