algbio/flowpaths

A Python package to quickly decompose weighted graphs into weights paths, under various models.

Language: Python - Size: 1.93 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 5 - Forks: 1

algbio/safe-sequences

Language: Python - Size: 27.3 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

algbio/SRFAligner

Language: C++ - Size: 265 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 13 - Forks: 0

algbio/founderblockgraphs

Constructs segment repeat-free founder block graphs from multiple sequence alignments

Language: C++ - Size: 167 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 1

algbio/SBWT

Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)

Language: C++ - Size: 6.09 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 24 - Forks: 6

algbio/KMC Fork of refresh-bio/KMC

A fork of KMC used in the SBWT repository https://github.com/algbio/SBWT

Language: C++ - Size: 2.78 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 4

algbio/emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

Language: C++ - Size: 1.44 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 17 - Forks: 0

algbio/ggcat

Compacted and colored de Bruijn graph construction and querying

Language: Rust - Size: 4.34 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 82 - Forks: 12

algbio/matchtigs

Minimum plain text representation of kmer sets

Language: Rust - Size: 313 KB - Last synced at: 3 days ago - Pushed at: 3 months ago - Stars: 17 - Forks: 5

algbio/themisto

Space-efficient pseudoalignment with a colored de Bruijn graph

Language: C++ - Size: 16.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 53 - Forks: 4

algbio/spl-IsoQuant

A pipeline for processing Spl-Iso-Seq data

Language: Python - Size: 56.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

algbio/optimized-fd

Language: Python - Size: 89.8 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

algbio/efg-mems

MEM finding on (elastic founder) graphs

Language: C++ - Size: 10.3 MB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

algbio/alignment-safety

Language: Jupyter Notebook - Size: 77.4 MB - Last synced at: 9 months ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0

algbio/panvc3-experiments

Experiments for evaluating PanVC 3

Language: Python - Size: 131 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

algbio/panvc-sample-workflow

Sample variant calling workflow using short reads for PanVC

Language: Python - Size: 231 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

algbio/GraphChainer-scripts

Language: Python - Size: 31.3 KB - Last synced at: 2 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

algbio/flowtigs

Language: Rust - Size: 73.2 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

algbio/Badger

Badger is a long read barcode calling tool

Language: Python - Size: 58.6 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

algbio/metaflow

MetaFlow is a program for community profiling of a metagenomic sample

Language: C++ - Size: 3.04 MB - Last synced at: about 1 year ago - Pushed at: about 9 years ago - Stars: 7 - Forks: 1

algbio/emerald-analysis

Language: Jupyter Notebook - Size: 349 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

algbio/panvc-founders

Instructions and examples for using PanVC with founder sequences

Language: Python - Size: 561 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

algbio/GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

Language: C++ - Size: 305 KB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 25 - Forks: 3

algbio/mfd-safety

Language: Python - Size: 84 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

algbio/anchors-in-chaining

Language: Python - Size: 23.5 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

algbio/sdsl-lite Fork of iosfwd/sdsl-lite

Fork of Succinct Data Structure Library 2.0 used in Themisto

Size: 8.9 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

algbio/GreedySuperstring

Greedy space-efficient construction of short approximate superstrings

Language: C++ - Size: 183 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

algbio/bdbwt

Bidirectional Burrows-Wheeler index

Language: C++ - Size: 1.75 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

algbio/PerformanceMPC

Language: C++ - Size: 4.82 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

algbio/flow-decomposition-safety

Language: Python - Size: 4.53 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

algbio/practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.

Language: Jupyter Notebook - Size: 4.44 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 0

algbio/br-index-mems Fork of U-Ar/br-index

MEM finding on texts and graphs using bidirectional r-index

Language: C++ - Size: 260 KB - Last synced at: 9 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

algbio/MFD-ILP

Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.

Language: Jupyter Notebook - Size: 791 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 0

algbio/SafePathsRNAPC

Language: Shell - Size: 115 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

algbio/bdbwt-mem-chaining

Language: C++ - Size: 16 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

algbio/Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

Size: 2.46 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 0

algbio/VOMM

Space-efficient variable-order Markov models

Language: C++ - Size: 1.91 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 5 - Forks: 0

algbio/bwtCluster

Space-efficient clustering for metagenomic reads

Language: C++ - Size: 146 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

algbio/teaching-materials

Teaching materials of the Algorithmic Bioinformatics Group @ University of Helsinki

Size: 13.7 KB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 1