FredHutch / microbial-rnaseq
Analysis of RNAseq data from (host-associated) microbial mixtures
☆12Updated 5 years ago
Alternatives and similar repositories for microbial-rnaseq:
Users that are interested in microbial-rnaseq are comparing it to the libraries listed below
- Accurate, Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes☆30Updated 8 months ago
- Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host…☆21Updated 10 months ago
- kASA - k-Mer Analysis of Sequences based on Amino acid-like encoding☆23Updated last year
- A shiny package for microbiome functional enrichment analysis☆37Updated 3 months ago
- Analyze a set of genomes with the anvi'o pangenome pipeline☆17Updated last year
- SAMsift: advanced filtering and tagging of SAM/BAM alignments using Python expressions.☆23Updated 6 years ago
- BACTpipe: An assembly and annotation pipeline for bacterial genomics☆20Updated 2 months ago
- R Interface to the NCBI SRA metadata☆23Updated 6 years ago
- SeqWho - A reliable and rapid FASTQ(A) file classifier☆11Updated 3 years ago
- Maximum Likelihood Amplicon Pipeline☆22Updated 8 months ago
- R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.☆23Updated last year
- ☆19Updated 7 years ago
- A program for fast and accurate genome-guided transcripts reconstruction and quantification from RNA-seq (Supporting Pacbio single-end)☆23Updated 3 years ago
- A command line tool to compute mapping statistics from a BAM file☆23Updated 2 years ago
- A comprehensive toolkit for running Oxford Nanopore's MinION☆12Updated 6 years ago
- De novo VIral Genome Annotator☆21Updated 5 months ago
- Do microbiome analysis with dada2 and phyloseq object☆12Updated 4 months ago
- transposable element typing pipeline☆17Updated 11 months ago
- (Obsolete) NCBI Prokaryotic Genome Annotation Pipeline. New site:☆15Updated 6 years ago
- Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database☆10Updated 8 years ago
- Handy tools for Microbiome analysis in R☆18Updated 5 years ago
- a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser☆13Updated 6 years ago
- fastq quality assessment and filtering tool☆18Updated 2 years ago
- easy_sbatch - Batch submitting Slurm jobs with script templates☆17Updated 3 years ago
- Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.☆15Updated 6 years ago
- Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop☆18Updated 9 years ago
- Highly sensitive pathogen detection☆12Updated 4 years ago
- Converts 'MultiQC' Reports into Tidy Data Frames☆18Updated 10 months ago
- A Shotgun Metagenome Annotation Pipeline☆23Updated 7 years ago
- CLI to automate Nextflow pipeline testing☆12Updated 2 months ago