Kristoffer

strobealign. Aligns short reads using dynamic seed size with strobemers

isONclust. De novo clustering of long transcript reads into genes

strobemers. A repository for generating strobemers and evalaution

NGSpeciesID. Reference-free clustering and consensus forming of long-read amplicon sequencing

ultra. Long-read splice alignment with high accuracy

isONcorrect. Error correction of ONT transcript reads

BESST. BESST - scaffolder for genomic assemblies

IsoCon. Derives consensus sequences from a set of long noisy reads by clustering and error correction.

BESST_RNA. Scaffolding of genomic assemblies with RNA seq data

namfinder. Finds Non-overlapping Approximate Matches (NAMs) between query and reference sequences using strobemers

GetDistr. Calculates distribution of observed fragment sizes (or insert sizes) in various scenarios for structural variant calling or genome assembly

pyinfor. some of my codes on bioinformatics with python

optimal_k. Calculates optimal k for a DBG assembler given one or more read libraries

IsoCon_Eval. Evaluation scripts for IsoCon + targeted sequencing approach

alignment_evaluation. Python

GapEst. Estimating distance of unknown sequence in genomic assemblies using paired read libraries (e.g. PE, MP)

isocon_nontargeted_eval. Python

genomics_tools. Misc scripts for information processing of genomes, reads, variants, etc..

old_webpage.github.io. HTML