DEploid-dev / DEploidLinks
dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.
☆21Updated last year
Alternatives and similar repositories for DEploid
Users that are interested in DEploid are comparing it to the libraries listed below
Sorting:
- Scaffolding genomes using synthetic long read clouds☆20Updated 9 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆46Updated 7 years ago
- reference free variant assembly☆34Updated 2 years ago
- Rapid competitive read demulitplexer. Made with tries.☆23Updated 8 months ago
- ☆28Updated 10 months ago
- Assembler for raw de novo genome assembly of long uncorrected reads.☆35Updated 6 years ago
- A simple tool to fix PacBio fasta/q that was not properly split into subreads☆16Updated 4 years ago
- Contains the description of a file format to store kmers and associated values☆34Updated 3 years ago
- Bam Read Index - Extract alignments from a bam file by readname☆28Updated last year
- Classify sequencing reads using MinHash.☆48Updated 5 years ago
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Updated 4 months ago
- REINDEER REad Index for abuNDancE quERy☆56Updated 7 months ago
- Symmetric DUST for finding low-complexity regions in DNA sequences☆45Updated 6 months ago
- Parallel implementation of the LAST aligner☆18Updated 9 years ago
- Benchmark MinION assembler pipelines and publish your results in a heartbeat!☆15Updated 5 years ago
- Fast in-silico normalization algorithm for NGS data☆23Updated 4 years ago
- Hitting associations with k-mers☆44Updated 3 years ago
- Preprocessing paired-end reads produced with experiment-specific protocols☆32Updated 7 years ago
- Reference-free variant discovery in large eukaryotic genomes☆42Updated 4 years ago
- Fast calculations of linkage-disequilibrium in large-scale human cohorts☆44Updated 6 years ago
- Exploration of controlled loss of quality values for compressing CRAM files☆36Updated 2 years ago
- Graphite - Graph-based variant adjudication☆28Updated 5 years ago
- simple bioinformatics command-line (t)ools (i) (w)ished (i) (h)ad.☆44Updated 2 years ago
- Find Unique genomic Regions☆32Updated 2 weeks ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 7 years ago
- Metagenomic profiling and phylogenetic distances via common kmers☆42Updated 4 years ago
- ☆18Updated 8 years ago
- Runs a combination of tools to generate structural variant calls on short-read whole-genome sequencing data☆22Updated 4 years ago
- Linear-time, low-memory construction of variation graphs☆20Updated 6 years ago
- Various scripts and recipes for working with nanopore data☆34Updated 9 years ago