USDA-ARS-GBRU / itsxpressLinks
Software to trim the ITS region of FASTQ sequences for amplicon sequencing analysis
☆15Updated 9 months ago
Alternatives and similar repositories for itsxpress
Users that are interested in itsxpress are comparing it to the libraries listed below
Sorting:
- workflows for offline analysis of 16S rRNA Nanopore data☆16Updated 2 years ago
- Bash pipeline for analysis of ONT full-length 16S sequences in QIIME2☆29Updated 5 years ago
- ☆56Updated 6 months ago
- PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples☆46Updated 2 years ago
- An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.☆49Updated 2 years ago
- PATO is a R package designed to analyze pangenomes (set of genomes) intra or inter species.☆62Updated 2 years ago
- Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.☆48Updated 9 months ago
- ☆75Updated last week
- Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes☆55Updated 2 months ago
- scripts for estimating bacteria replication rates based on population genome copy number variation☆73Updated 6 years ago
- A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing☆69Updated 4 years ago
- IS mapping software☆57Updated 4 years ago
- phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.☆88Updated 2 years ago
- MicrobeCensus estimates the average genome size of microbial communities from metagenomic data☆47Updated 5 years ago
- GTDB taxonomy taxdump files with trackable TaxIds☆56Updated 8 months ago
- Horizontal gene transfer (HGT) identification pipeline☆65Updated 2 years ago
- Spaghetti: in situ analysis of 16S rRNA amplicons obtained by nanopore sequencing☆19Updated last year
- SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customi…☆61Updated last year
- A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during…☆82Updated 3 months ago
- Teaching materials for SymbNET course: from MAGs to GEMs☆14Updated last year
- A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs☆32Updated 3 weeks ago
- Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)☆61Updated 2 years ago
- ☆84Updated 2 years ago
- Microbial Populations as Clusters Of Gene Transfer☆45Updated 2 years ago
- Contains a fasta format database of a large variety of mobile genetic elements and an annotation file☆52Updated 4 years ago
- Improvement of metagenome-assembled genomes☆54Updated 5 years ago
- A pipeline for the identification of fungi in public metagenomics datasets☆17Updated 5 years ago
- Ley Lab MetaGenome Profiler DataBase generator☆50Updated 3 years ago
- The Prokaryotic Genomics and Comparative Genomics Analysis Pipeline☆41Updated 3 years ago
- SynTracker is a pipeline, designated to determine the biological relatedness of conspecific strains (microbial strains of the same specie…☆39Updated 3 months ago