ksahlin

strobealign

Aligns short reads using dynamic seed size with strobemers

strobemers

A repository for generating strobemers and evalaution

ultra

Long-read splice alignment with high accuracy

BESST

BESST - scaffolder for genomic assemblies

isONcorrect

Error correction of ONT transcript reads

NGSpeciesID

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

isONclust

De novo clustering of long transcript reads into genes

BESST_RNA

Scaffolding of genomic assemblies with RNA seq data

IsoCon

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

GetDistr

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

namfinder

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

pyinfor

some of my codes on bioinformatics with python

IsoCon_Eval

Evaluation scripts for IsoCon + targeted sequencing approach

optimal_k

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

alignment_evaluation

genomics_tools

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

isocon_nontargeted_eval

isONform

De novo construction of isoforms from long-read data

old_webpage.github.io

cDNA_primer

Scripts for processing PacBio transcriptome (Iso-Seq) data

edlib

Lightweight, super fast C/C++ library for sequence alignment using edit (Levenshtein) distance.

eval_Gap2Seq

Evaluation pipeline for Gap2Seq written in snakemake

eval_kmer_choice

Evaluates the best k-mer choice from programs choosing an optimal k in De Bruijn graphs

generate_assembly

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

mathstats

Contains mathematical and statistical functions, distributions, tests.

mixedstrobes_altstrobes

Updated analysis scripts for new strobemer members mixedstrobes and altstrobes

pychopper

A tool to identify full length cDNA reads

slaMEM

Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array

ssw

Python interface for SIMD Smith-Waterman Library

svsim

Simulation toolbox for structural variations.