Tagged bioinformatics

Delimit species from molecular data with ASAP, mPTP and GMYC

Query the Ensembl REST API for genes, sequences, variant effects and orthologs

Find cross-database links between NCBI records like genes, proteins and papers

Detect antimicrobial resistance genes and mutations in bacterial genomes

Type bacterial isolates with MLST, cgMLST and serotyping for outbreak work

Estimate pathogen phylogeny timing and reproduction numbers with TreeTime and BEAST2

Infer person-to-person pathogen transmission links from genome data

Assign pathogen lineages and track variant frequencies with Pangolin and Nextstrain

Call m6A RNA methylation peaks from MeRIP-seq IP and input pairs

Detect m6A RNA modifications from Nanopore direct RNA sequencing with m6Anet

Plot RNA modification metagene profiles, peak heatmaps and browser tracks

Balance batches against biology so genomics experiments stay estimable

Control false discovery rates across thousands of genomic tests

Calculate power for high-dimensional genomics experiments with count models

Design genomics experiments with randomization, blocking and proper replication

Estimate replicate numbers for target power and FDR in genomics experiments

Import count matrices from featureCounts, STAR, Salmon and 10X into R or Python

Map gene IDs across Ensembl, Entrez, HGNC, UniProt and RefSeq systems

Normalize and transform RNA-seq counts with TMM, VST and log-CPM

Store and operate on sparse single-cell expression matrices efficiently

Call germline variants with GATK HaplotypeCaller and GVCF joint genotyping

Build weighted gene co-expression networks to find modules and hub genes

Compare gene networks between conditions to find rewired gene relationships

Infer gene regulatory networks with ARACNe, GENIE3 and VIPER activity

Build enhancer-driven gene regulatory networks from scRNA-seq and ATAC-seq

Simulate transcription factor knockdowns in silico and predict perturbation responses

Infer single-cell transcription factor regulons and activity with pySCENIC

Score genome annotation completeness with BUSCO, OMArk and CheckM2

Transfer gene annotations between genome assemblies with liftover and Liftoff

Predict eukaryotic gene structures with BRAKER3, GALBA and Helixer

Assign GO terms, protein domains and KEGG orthologs to predicted proteins

Find noncoding RNAs like tRNA, rRNA and riboswitches with Infernal and tRNAscan

Annotate bacterial genomes and plasmids with Bakta or Prokka for submission

Mask and classify repeats and transposable elements with RepeatModeler2 and EDTA

Polish draft genome assemblies with Racon, medaka and Polypolish to raise accuracy

Assess genome assembly contiguity, completeness and correctness with BUSCO and Merqury

Find and remove foreign sequence contamination in genome assemblies with FCS-GX

Estimate genome size, heterozygosity and ploidy from reads with GenomeScope2

Assemble haplotype-resolved and T2T genomes from PacBio HiFi reads with hifiasm

Assemble genomes from noisy Nanopore or PacBio CLR reads with Flye and Canu

Assemble metagenomes into MAGs from long or short reads with metaFlye and MEGAHIT

Scaffold contigs into chromosome-scale sequences with Hi-C data using YaHS

Assemble genomes from Illumina short reads with SPAdes, MEGAHIT and Unicycler

Design base editor guides with the target base set inside the editing window

Design and rank CRISPR guide RNAs for knockout with PAM scanning and filters

Design donor templates for precise CRISPR knock-ins with homology arms and blocking edits

Predict CRISPR off-target sites genome-wide with CFD scores and variant screening

Design pegRNAs and nicking guides for prime editing with PBS and RTT tuning

Read and convert BED interval files with coordinate conventions handled