algbio/SBWT algbio/SBWT

  • Stars
    star
    23
  • Rank 1,016,462 (Top 21 %)
  • Language
    C++
  • License
    GNU General Publi...
  • Created over 2 years ago
  • Updated 3 months ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
algbio/SBWT
github

algbio

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

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

More Repositories

1

themisto

Space-efficient pseudoalignment with a colored de Bruijn graph
C++
50
star
2

GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining
C++
30
star
3

matchtigs

Minimum plain text representation of kmer sets
Rust
17
star
4

emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space
C++
16
star
5

MFD-ILP

Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.
Jupyter Notebook
12
star
6

metaflow

MetaFlow is a program for community profiling of a metagenomic sample
C++
7
star
7

VOMM

Space-efficient variable-order Markov models
C++
5
star
8

PerformanceMPC

Efficient C++ implementations of different fast algorithms for Minimum Path Cover
C++
5
star
9

mfd-safety

Python
4
star
10

emerald-analysis

Jupyter Notebook
3
star
11

Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)
3
star
12

practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.
Jupyter Notebook
3
star
13

optimized-fd

Python
2
star
14

RobustFlowDecomposition

Flow Decomposition Under Uncertainty
Python
2
star
15

SRFAligner

C++
2
star
16

spl-IsoQuant

A pipeline for processing Spl-Iso-Seq data
Python
1
star
17

anchors-in-chaining

Python
1
star
18

panvc-founders

Instructions and examples for using PanVC with founder sequences
Python
1
star
19

bwtCluster

Space-efficient clustering for metagenomic reads
C++
1
star
20

alignment-safety

Jupyter Notebook
1
star
21

founderblockgraphs

Constructs segment repeat-free founder block graphs from multiple sequence alignments
C++
1
star
22

efg-mems

MEM finding on (elastic founder) graphs
C++
1
star
23

panvc3-experiments

Experiments for evaluating PanVC 3
Python
1
star