Pinned Repositories
practical-omnitigs
A repository to conduct experiments with omnitig-related models for genome assembly.
abstract-datastructures-rs
Some traits defining data structures
bcalm
compacted de Bruijn graph construction in low memory
bifrost
Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
bigraph-rs
Represent bigraphs in an abstract manner.
bioconda-recipes
Conda recipes for the bioconda channel.
compact-genome-rs
Bit-packed genome storage
genome-graph-rs
Types as well as IO functions for genome graphs.
homopolymer-compress-rs
Homopolymer compression of genomic data.
omnitigs-rs
Implementations of omnitig related algorithms.
sebschmi's Repositories
sebschmi/abstract-datastructures-rs
Some traits defining data structures
sebschmi/bigraph-rs
Represent bigraphs in an abstract manner.
sebschmi/compact-genome-rs
Bit-packed genome storage
sebschmi/genome-graph-rs
Types as well as IO functions for genome graphs.
sebschmi/homopolymer-compress-rs
Homopolymer compression of genomic data.
sebschmi/omnitigs-rs
Implementations of omnitig related algorithms.
sebschmi/bifrost
Bifrost: Highly parallel construction and indexing of colored and compacted de Bruijn graphs
sebschmi/bioconda-recipes
Conda recipes for the bioconda channel.
sebschmi/codegen-course
sebschmi/fastx-statistics-rs
Rust tool to compute basic statistics of fasta or fastq files.
sebschmi/flowtigs
sebschmi/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
sebschmi/ggcat
Compacted and colored de Bruijn graph construction and querying
sebschmi/HI.SIM
HiFi error modeler and simulator with ploidy
sebschmi/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
sebschmi/minimap2-homopolymer-decompression
Homopolymer decompress minimap alignments
sebschmi/minimap2-paf-io
Read and write files in minimap2's PAF format.
sebschmi/minimizer-iterator-rs
An iterator over the minimizers of a sequence.
sebschmi/node-to-arc-centric-dbg
Convert a node-centric DBG into an arc-centric one
sebschmi/prophasm
ProphAsm – a tool for computing simplitigs and k-mer sets manipulation
sebschmi/quast
A fork of the popular QUAST genome assembly evaluator to incorporate more advanced metrics
sebschmi/random-dna-generator-rs
Generate random DNA sequences for debugging bioinfo software
sebschmi/rust-mdbg
minimizer-space de Bruijn graphs (mdBG) for whole genome assembly
sebschmi/safe-paths-with-flowtigs
sebschmi/select-random-fastx
Select random records from fasta/fastq files
sebschmi/short-range-template-switching
Computational methods for the manuscript: Thousands of human mutation clusters are explained by short-range template switching
sebschmi/snakemake-turso
Snakemake project template that can be executed on the turso federation (ukk02/vorna/...)
sebschmi/verify-same-kmer-content
Verify that two given GFA or fasta files have the same kmer content
sebschmi/wtdbg2
Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly
sebschmi/wtdbg2-homopolymer-decompression
Replace homopolymer compressed reads in wtdbg2's .ctg.lay file with decompressed reads.