Pinned Repositories
BESST
BESST - scaffolder for genomic assemblies
BESST_RNA
Scaffolding of genomic assemblies with RNA seq data
GetDistr
Calculates distribution of observed fragment sizes (or insert sizes) in various scenarios for structural variant calling or genome assembly
IsoCon
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
isONclust
De novo clustering of long transcript reads into genes
isONcorrect
Error correction of ONT transcript reads
NGSpeciesID
Reference-free clustering and consensus forming of long-read amplicon sequencing
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
ksahlin's Repositories
ksahlin/strobealign
Aligns short reads using dynamic seed size with strobemers
ksahlin/strobemers
A repository for generating strobemers and evalaution
ksahlin/ultra
Long-read splice alignment with high accuracy
ksahlin/BESST
BESST - scaffolder for genomic assemblies
ksahlin/isONcorrect
Error correction of ONT transcript reads
ksahlin/NGSpeciesID
Reference-free clustering and consensus forming of long-read amplicon sequencing
ksahlin/isONclust
De novo clustering of long transcript reads into genes
ksahlin/BESST_RNA
Scaffolding of genomic assemblies with RNA seq data
ksahlin/IsoCon
Derives consensus sequences from a set of long noisy reads by clustering and error correction.
ksahlin/GetDistr
Calculates distribution of observed fragment sizes (or insert sizes) in various scenarios for structural variant calling or genome assembly
ksahlin/namfinder
Finds Non-overlapping Approximate Matches (NAMs) between query and reference sequences using strobemers
ksahlin/pyinfor
some of my codes on bioinformatics with python
ksahlin/IsoCon_Eval
Evaluation scripts for IsoCon + targeted sequencing approach
ksahlin/optimal_k
Calculates optimal k for a DBG assembler given one or more read libraries
ksahlin/alignment_evaluation
ksahlin/genomics_tools
Misc scripts for information processing of genomes, reads, variants, etc..
ksahlin/isocon_nontargeted_eval
ksahlin/isONform
De novo construction of isoforms from long-read data
ksahlin/old_webpage.github.io
ksahlin/cDNA_primer
Scripts for processing PacBio transcriptome (Iso-Seq) data
ksahlin/edlib
Lightweight, super fast C/C++ library for sequence alignment using edit (Levenshtein) distance.
ksahlin/eval_Gap2Seq
Evaluation pipeline for Gap2Seq written in snakemake
ksahlin/eval_kmer_choice
Evaluates the best k-mer choice from programs choosing an optimal k in De Bruijn graphs
ksahlin/generate_assembly
Generates a genome from a markov model, PE and MP reads, a contig assembly and a mapping of reads to contigs
ksahlin/mathstats
Contains mathematical and statistical functions, distributions, tests.
ksahlin/mixedstrobes_altstrobes
Updated analysis scripts for new strobemer members mixedstrobes and altstrobes
ksahlin/pychopper
A tool to identify full length cDNA reads
ksahlin/slaMEM
Finding Maximal Exact Matches (MEMs) using a Sampled LCP Array
ksahlin/ssw
Python interface for SIMD Smith-Waterman Library
ksahlin/svsim
Simulation toolbox for structural variations.