tanaes / snakemake_assemble
Modular snakemake workflow for assembly-based metagenomics
☆10Updated 7 years ago
Alternatives and similar repositories for snakemake_assemble:
Users that are interested in snakemake_assemble are comparing it to the libraries listed below
- Horizontal Gene Transfer Detection by Mapping Sequencing Reads☆21Updated 7 years ago
- Tools for extracting individual genomes from metagenomes☆17Updated last year
- Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes☆27Updated 7 years ago
- Annotate your metagenome assemblies☆11Updated 6 years ago
- Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI☆29Updated 6 years ago
- Assembly based core genome SNP alignments for bacteria☆25Updated 5 years ago
- 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
- A Shotgun Metagenome Annotation Pipeline☆23Updated 7 years ago
- Strain-level abundances estimation in metagenomic samples using variation graphs☆25Updated 2 years ago
- Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database☆10Updated 8 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
- A repository with scripts to run pipeline that are commonly used in the Meren Lab☆11Updated 6 years ago
- Detect contigs of complete circular genomes☆22Updated 5 years ago
- Metagenomic binning suite☆29Updated 2 years ago
- a Contig Alignment Tool for Pairwise Assembly Comparison☆13Updated 5 years ago
- Output FASTQ summary statistics in JSON format☆29Updated 2 years ago
- Utility to analyse a group of closely related MAgs/Genomes/bins/SUBs of more or less dubious origin☆12Updated 4 months ago
- MAG Circularization Method☆33Updated 2 years ago
- ☆22Updated last year
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 8 years ago
- Utility program for extracting sequences from a fasta/fastq file☆36Updated last month
- Assembly by Reduced Complexity (ARC)☆41Updated 8 years ago
- Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database☆40Updated 4 years ago
- FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of mic…☆24Updated 3 years ago
- Reference Phylogeny for Bacterial and Archaeal Genomes☆25Updated last year
- Strain Prediction and Analysis with Representative SEquence☆18Updated last month
- A pipeline for performing genome-wide association tests for bacterial genomes.☆27Updated 6 years ago
- Quickly get the taxonomy of a genome☆10Updated last year
- Interactive tools for metagenome visualization and binning in R☆28Updated 6 years ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year