maxibor / sam2lca
Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
☆9Updated 3 months ago
Related projects ⓘ
Alternatives and complementary repositories for sam2lca
- software to identify primers that can distinguish genomes☆20Updated 3 weeks ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- QA/QC pipeline for a MiSeq/HiSeq/Ion Torrent/assembly-only run☆11Updated 2 months ago
- Strain-level taxonomic classification of metagenomic data using pangenome graphs☆16Updated this week
- De novo VIral Genome Annotator☆21Updated 2 months ago
- ☆16Updated last month
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆14Updated 2 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 2 years ago
- pipeline for read mapping, snp calling and annotation for bacterial genomes☆11Updated 8 months ago
- screening metagenomes for arbitrary lineages, using gene-centric assembly methods and phylogenetics☆11Updated 4 years ago
- transposable element typing pipeline☆17Updated 8 months ago
- Read contamination removal☆24Updated 10 months ago
- MetagenOmic read Re-Assigner and abundance quantifier☆18Updated 5 months ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- metagenome population recombination rate estimation pipeline☆12Updated 3 months ago
- Indels are not ideal - quick test for interrupted ORFs in bacterial/microbial genomes☆15Updated 6 years ago
- Mycobacterium tuberculosis genomic analysis from Nanopore sequencing data☆11Updated 5 months ago
- Variant call verification☆15Updated last year
- Visualisation application for Klebsiella genotypes generated by Kleborate.☆9Updated 3 years ago
- Code to create a PRG from a Multiple Sequence Alignment file☆22Updated 7 months ago
- Dadaist2 🟨 Highway to R☆13Updated 9 months ago
- Map query sequences to the assemblies of all pre-June 2023 bacteria (https://ftp.ebi.ac.uk/pub/databases/AllTheBacteria/Releases/0.2/) on…☆12Updated 6 months ago
- A containerized bioinformatics pipeline for viral metagenomic data analysis☆25Updated 3 months ago
- A pipeline for whole genome assembly☆16Updated 2 years ago
- ☆17Updated 5 months ago
- Non-redundant pangenome assemblies from multiple genomes or bins☆13Updated 3 months ago
- Strain-level haplotyping for metagenomes with short or long-reads.☆41Updated 4 months ago
- Remove human reads from a sequencing run☆24Updated last month
- GRIMER performs analysis of microbiome studies and generates a portable and interactive dashboard integrating annotation, taxonomy and me…☆21Updated last year
- Plot genome alignment figure using progressiveMauve & genoPlotR☆21Updated 2 years ago