seqan / needle
A fast and space-efficient pre-filter for estimating the quantification of very large collections of nucleotide sequences
☆14Updated this week
Related projects ⓘ
Alternatives and complementary repositories for needle
- exploring viral genome assembly with variation graph tools☆19Updated 4 years ago
- Sequence Distance Graph framework: graph + reads + mapping + analysis☆25Updated 2 years ago
- Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.☆24Updated 3 years ago
- A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)☆14Updated 3 years ago
- Minimizer-based assembly scaffolding and mapping using long reads☆31Updated last month
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆11Updated 8 months ago
- Library for the Handle Graph abstraction☆21Updated 4 months ago
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers☆21Updated 4 years ago
- GBWT-based handle graph☆30Updated 2 weeks ago
- ProphAsm – a rapid computation of simplitigs directly from k-mer sets☆26Updated last year
- An experimental tool to find approximate max-cuts in a large graph☆11Updated 3 years ago
- Toolkit for manipulating FASTA and SAM files☆17Updated 8 months ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 5 years ago
- Python bindings for Bifrost with a NetworkX compatible API☆27Updated last year
- ☆10Updated 3 years ago
- C++ library for parsing several formats in bioinformatics☆9Updated last year
- Classify sequencing reads using MinHash.☆48Updated 4 years ago
- ☆28Updated last year
- Small general purpose library for C and Python with focus on bioinformatics.☆29Updated 2 years ago
- Construct a Physical Map from Linked Reads☆18Updated 7 months ago
- Python bindings to minimap2☆16Updated 7 years ago
- Linear-time, low-memory construction of variation graphs☆18Updated 4 years ago
- Histosketching Using Little Kmers☆55Updated last year
- This repo is deprecated. Please use gfatools instead.☆16Updated 6 years ago
- An experimental tool to estimate the similarity between all pairs of contigs☆35Updated 3 years ago
- Preprocessing paired-end reads produced with experiment-specific protocols☆32Updated 6 years ago
- deBGR: An Efficient and Near-Exact Representation of the Weighted de Bruijn Graph☆30Updated 3 years ago