iqbal-lab-org / make_prg
Code to create a PRG from a Multiple Sequence Alignment file
☆22Updated 7 months ago
Related projects ⓘ
Alternatives and complementary repositories for make_prg
- Strain-level haplotyping for metagenomes with short or long-reads.☆39Updated 4 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Plasmid analysis using rearrangement distances☆29Updated 2 months ago
- Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)☆25Updated 6 months ago
- Differential k-mer analysis☆33Updated 9 months ago
- Sequence-independent identification and removal of adapters/systemic contamination in shotgun sequencing data. https://doi.org/10.1093/bi…☆16Updated last year
- Colinear block visualisation tool☆30Updated 9 months ago
- Haplotype-aware genome assembly toolkit☆29Updated 4 years ago
- A mathematically characterized hypothesis test for organism presence/absence in a metagenome☆30Updated this week
- recompute GFA link overlaps☆25Updated 2 years ago
- ☆21Updated last month
- Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.☆33Updated last week
- A pipeline for bioinformatics analysis of bacterial genomes☆19Updated 4 months ago
- Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes☆31Updated 3 weeks ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 3 months ago
- Scaffolding with Ultralong Reads☆14Updated 3 years ago
- a tool to filter sites in a FASTA-format whole-genome pseudo-alignment☆37Updated last month
- software to identify primers that can distinguish genomes☆20Updated this week
- Variant call verification☆15Updated last year
- Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]☆19Updated 7 months ago
- CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies☆24Updated 4 years ago
- ☆15Updated 4 years ago
- VStrains is a de novo approach for reconstructing strains from viral quasispecies.☆22Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- MetagenOmic read Re-Assigner and abundance quantifier☆17Updated 4 months ago
- Intra-species bacterial contamination detection☆22Updated last year
- Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s).☆24Updated 7 months ago
- StrainXpress is a de novo assembly method which base on overlap-layout-consensus (OLC) paradigm and can fast and accurately assemble high…☆13Updated 8 months ago
- Rapid and simple taxonomic profiling of genome and metagenome contigs☆27Updated last year