CMU-SAFARI / Apollo
Apollo is an assembly polishing algorithm that attempts to correct the errors in an assembly. It can take multiple set of reads in a single run and polish the assemblies of genomes of any size. Described in the Bioinformatics journal paper (2020) by Firtina et al. at https://people.inf.ethz.ch/omutlu/pub/apollo-technology-independent-genome-asse…
☆27Updated 4 years ago
Alternatives and similar repositories for Apollo:
Users that are interested in Apollo are comparing it to the libraries listed below
- AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shar…☆27Updated 11 months ago
- BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy…☆43Updated last year
- ☆28Updated 3 weeks ago
- Minimizer-based assembly scaffolding and mapping using long reads☆39Updated 6 months ago
- Close assembly gaps using long-reads at high accuracy.☆48Updated last year
- FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: http…☆26Updated 2 years ago
- Lift-over alignments from variant-aware references☆34Updated 2 years ago
- An experimental tool to estimate the similarity between all pairs of contigs☆35Updated 4 years ago
- De Bruijn graph construction for large k.☆18Updated 3 years ago
- URMAP ultra-fast read mapper☆38Updated 4 years ago
- Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improveme…☆37Updated last year
- Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.☆22Updated 6 years ago
- An algorithm for centromere assembly using long error-prone reads☆26Updated 3 years ago
- GeneMark-ETP: gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology☆21Updated 3 weeks ago
- A streaming method for mapping nanopore raw signals☆32Updated 3 years ago
- Proof-of-concept implementation of GWFA for sequence-to-graph alignment☆57Updated 11 months ago
- GFA visualizer, GPU-accelerated using Vulkan☆70Updated 2 years ago
- PECAT, a phased error correct and assembly tool☆49Updated last week
- Economic Genome Assembly from Low Coverage Illumina and Nanopore Data☆19Updated 3 years ago
- tandem repeat finding from erroneous long reads☆15Updated 3 years ago
- Metalign: efficient alignment-based metagenomic profiling via containment min hash☆33Updated last year
- Standalone tool and library allowing to work with barcoded linked-reads☆12Updated 5 months ago
- Tool for assessing/improving assembly quality in extra-long tandem repeats☆46Updated 4 years ago
- Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]☆12Updated last year
- Exact Tandem Repeat Finder (not a TRF replacement)☆49Updated 5 years ago
- Construct a Physical Map from Linked Reads☆18Updated last year
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- ☆14Updated last year
- recompute GFA link overlaps☆25Updated 2 years ago
- base-accurate DNA sequence alignments using edlib and mashmap2☆33Updated 4 years ago