tanaes / snakemake_assemble
Modular snakemake workflow for assembly-based metagenomics
☆10Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for snakemake_assemble
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆20Updated 7 years ago
- Tools for extracting individual genomes from metagenomes☆17Updated 11 months ago
- Advanced metagenomic Sequence Analysis in R☆15Updated 6 years ago
- ☆21Updated last year
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated last year
- Utility program for extracting sequences from a fasta/fastq file☆36Updated 7 months ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 5 years ago
- TAXnomic Profile Aggregation and STAndardisation☆34Updated last week
- Metagenomic species profiling with enhanced coverage of the human gut microbiome☆24Updated 5 months ago
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 6 years ago
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- Annotate your metagenome assemblies☆11Updated 6 years ago
- Scripts required to calculate tetramer frequencies and create input files for ESOM. See: Dick, G.J., A. Andersson, B.J. Baker, S.S. Simmo…☆17Updated 2 years ago
- Snakemake-based amplicon processing protocol for 16S and ITS sequences.☆14Updated 7 months ago
- Toolkit for establishing, updating, and validating GTDB species clusters☆20Updated 3 weeks ago
- Tools for analyzing trees☆14Updated 11 months ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Updated last year
- PARTIE is a program to partition sequence read archive (SRA) metagenomics data into amplicon and shotgun data sets. The user-supplied ann…☆25Updated last year
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆23Updated 3 years ago
- VIRULIGN: fast codon-correct alignment and annotation of viral genomes☆29Updated 3 years ago
- a Contig Alignment Tool for Pairwise Assembly Comparison☆12Updated 4 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Strain Prediction and Analysis with Representative SEquence☆18Updated last week
- Provides a local database of in-house and published genomes for Bacteria and Archaea from NCBI☆24Updated 10 years ago
- CAMITAX: Taxon labels for microbial genomes☆29Updated 10 months ago
- MiCoP is a method for high-accuracy profiling of viral and fungal metagenomic communities.☆14Updated 2 years ago
- Haplotype-aware genome assembly toolkit☆29Updated 4 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year