Repositório para materiais e documentos usados na II ELAB

High accuracy RAG for answering questions from scientific documents with citations

Snakemake workflow to detect and classify viruses in metagenome assemblies.

CAT/BAT/RAT: tools for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) and for taxonomic profiling of metagenomes

Fast genome-wide functional annotation through orthology assignment

The construction of reference gene catalog and metagenome-assembled genomes of pig gut microbiome.

Virus Identification By iteRative ANnoTation

Run virfinder in parallel

customizable pipeline to identify viral sequences from (meta)genomic data

create a interactive coverage plot dashboard from bam files and add gb, vcf and bed tracks

Pipeline to predict miRNAs from host affecting metagenome sequences

Scripts for analyses of deep subsurface drill core metagenomic and metatranscriptomic datasets from the Guaymas Basin, Mexico as part of the International Ocean Discovery Program Expedition 385.

Foreign Contamination Screening caller scripts and documentation

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1

Scripts and files for the annual Short Read Analysis Workshop

Snakemake pipeline calculating KEGG orthologue abundance in metagenomic sequence data.

FlexTaxD (Flexible Taxonomy Databases) - Create, add, merge different taxonomy sources (QIIME, GTDB, NCBI and more) and create metagenomic databases (kraken2, ganon and more )

Creation of a database of Genbank genomes including isolate reference genomes and MAGs, and parallelizing 1000s of genome searches for a specific marker

Analysing Metagenomic Species (MGS)

This pipeline is used for searching for hydrogenase genes from rumen metagenome and metatranscriptome data. The pipeline will create reference database using fasta file, then analyse the raw sequen…

Extracting, refining, and utilizing MAGs from EBPR reactor metagenomic time-series

Seurat meets tidyverse. The best of both worlds.

Code publicly

Robs manual for the computational genomics and bioinformatics class.

Pan-genomics of metagenome-assembled genomes suffers from fragmentation and incompleteness

Linking MAGs with 16S rRNA marker genes

Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data