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alignment_evaluation

besst

BESST - scaffolder for genomic assemblies

besst_rna

Scaffolding of genomic assemblies with RNA seq data

besst_s

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

eval_sv_tools

Benchmarks a range of different sv callers using snakemake for the workflow

gapest

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

generate_assembly

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

genomics_tools

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

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.

isocon_eval

Evaluation scripts for IsoCon + targeted sequencing approach

isocon_nontargeted_eval

isonclust

De novo clustering of long transcript reads into genes

isoncorrect

Error correction of ONT transcript reads

isonform

De novo construction of isoforms from long-read data

mathstats

Contains mathematical and statistical functions, distributions, tests.

mixedstrobes_altstrobes

Updated analysis scripts for new strobemer members mixedstrobes and altstrobes

namfinder

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

ngspeciesid

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

old_webpage.github.io

optimal_k

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

pychopper

A tool to identify full length cDNA reads

pyinfor

some of my codes on bioinformatics with python

python_koans

Python Koans - Learn Python through TDD

sahlin

Python course example at SciLifeLab

scaffolder

Scaffolder for genomic data