Aligns short reads using dynamic seed size with strobemers

Miscellaneous stuff

De novo clustering of long transcript reads into genes

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

Long-read splice alignment with high accuracy

A repository for generating strobemers and evalaution

Error correction of ONT transcript reads

BESST - scaffolder for genomic assemblies

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

Evaluation scripts for IsoCon + targeted sequencing approach

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

Evaluation pipeline for Gap2Seq written in snakemake

Contains mathematical and statistical functions, distributions, tests.

some of my codes on bioinformatics with python

Generates a genome from a markov model, PE and MP reads, a contig assembly and a mapping of reads to contigs

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

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