DEploid-dev / DEploid
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.
☆20Updated 3 weeks ago
Alternatives and similar repositories for DEploid:
Users that are interested in DEploid are comparing it to the libraries listed below
- Symmetric DUST for finding low-complexity regions in DNA sequences☆34Updated last year
- ☆28Updated last year
- Assembler for raw de novo genome assembly of long uncorrected reads.☆37Updated 5 years ago
- PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF f…☆30Updated 2 years ago
- Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.☆47Updated 6 years ago
- Exact Tandem Repeat Finder (not a TRF replacement)☆47Updated 5 years ago
- URMAP ultra-fast read mapper☆38Updated 4 years ago
- Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata☆56Updated 2 years ago
- Rapid competitive read demulitplexer. Made with tries.☆23Updated last year
- a toolset for fast DNA read set matching and assembly using a new type of reduced kmer☆37Updated 3 years ago
- Comprehensive alignment, whole-genome coverage, and capture coverage statistics.☆19Updated last month
- Population-wide Deletion Calling☆35Updated 4 months ago
- Collection of utilities for working with PacBio-based assemblies☆13Updated last year
- Contains the description of a file format to store kmers and associated values☆32Updated 2 years ago
- Exploration of controlled loss of quality values for compressing CRAM files☆34Updated last year
- Implementation of ToL genome assembly workflows☆20Updated 2 months ago
- Pipeline for structural variant image curation and analysis.☆48Updated 3 years ago
- Work for the tree sequence inference paper.☆23Updated 4 years ago
- My experimental tools on top of htslib. NOT OFFICIAL!!!☆54Updated last year
- Pipeline code for creating a fully haplotype-resolved assembly from a combination of PacBio/ONT long reads and Illumina Strand-seq data☆15Updated 9 months ago
- A simple tool to fix PacBio fasta/q that was not properly split into subreads☆14Updated 3 years ago
- Identifying repeats in high-throughput sequencing data☆15Updated 9 months ago
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Updated 6 years ago
- a simple C++ library for parsing and manipulating VCF files, + many command-line utilities☆19Updated 7 years ago
- Assembly by Reduced Complexity (ARC)☆41Updated 8 years ago
- A long-read analysis toolbox for cancer and population genomics☆21Updated 10 months ago
- REINDEER REad Index for abuNDancE quERy☆57Updated 5 months ago
- GFA insert into GenomicSQLite☆48Updated 3 years ago
- Method to optimally select samples for validation and resequencing☆27Updated 3 years ago