USDA-ARS-GBRU / itsxpress
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
☆12Updated last week
Related projects ⓘ
Alternatives and complementary repositories for itsxpress
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆27Updated 4 years ago
- ☆57Updated this week
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆58Updated last year
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆62Updated last year
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆37Updated 4 years ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆43Updated last year
- Nextflow pipeline to analyze PacBio HiFi full-length 16S data☆63Updated 11 months ago
- IS mapping software☆51Updated 2 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆49Updated 6 months ago
- ☆79Updated last year
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 3 years ago
- Synteny Imager☆60Updated 2 months ago
- Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWoo…☆47Updated 2 years ago
- ☆45Updated 7 months ago
- Assembly methods for nanopore-based metagenomic sequencing: a comparative study☆19Updated 4 years ago
- BEAV: Bacterial Element Annotation reVamped☆59Updated 3 weeks ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆43Updated 4 years ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆68Updated 4 years ago
- zol (& fai): large-scale targeted detection and evolutionary investigation of gene clusters (i.e. BGCs, phages, etc.)☆49Updated this week
- Add new taxa or taxonomic groups to the NCBI Taxdump files☆19Updated 4 years ago
- A toolbox for comparative genomics.☆97Updated 3 years ago
- Recovery of prokaryotic genomes from shotgun metagenomic sequencing data☆57Updated 3 years ago
- Materials and presentation for the 2023 ISB Microbiome course.☆24Updated last month
- Detection of pseudogene candidates in bacterial and archaeal genomes.☆45Updated 8 months ago
- Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more☆26Updated last year
- whole genome MLST analysis☆38Updated 6 months ago
- Inferring bacterial recombination rates from large-scale sequencing datasets.☆41Updated last year
- post processing of bacterial pangenome gene presence/absence matrices☆52Updated 2 months ago
- nanodisco: a toolbox for discovering and exploiting multiple types of DNA methylation from individual bacteria and microbiomes using nano…☆67Updated 2 years ago
- Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focu…☆49Updated last month