Many tools are available for various tasks in plant genomics. Finding the right tool for a certain purpose can be challenging. This repository provides an overview of available (and recommended) tools in plant genomics. This repository combines the experiences of the Plant Biotechnology and Biotechnology research group at TU Braunschweig. If you are new to plant genomics, our 'Data Literacy in Plant Genomics' course might be of interest to you.
| ToolName | Comments | Reference |
|---|---|---|
| guppy | ONT basecalling | ONT |
| fastQC | quality control short reads | FastQC GitHub repository |
| LongQC | quality control long reads | Fukasawa et al., 2020 |
| Filtlong | trimming long reads | Filtlong GitHub repository |
| Trimmomatic | trimming short reads | Bolger et al., 2014 |
| ToolName | Comments | Reference |
|---|---|---|
| MGSE | mapping-based | Pucker, 2019 |
| GenomeScope2 | k-mer-based | Ranallo-Benavidez, 2020 |
| findGSE | k-mer-based | Sun et al., 2017 |
| gnodes | mapping-based | Gilbert, 2022 |
| ToolName | Comments | Reference |
|---|---|---|
| HiCanu | long read assembler (resource intensive) | Nurk et al., 2020 |
| NextDenovo2 | long read assembler | GitHub repository |
| Shasta | long read assembler (fast) | Shafin et al., 2020 |
| Flye | long read assembler (high memory requirements) | Kolmogorov et al., 2019 |
| miniasm | long read assembler | Li, 2018 |
| QUAST | assembly statistics calculation | Gurevich et al., 2013 |
| Merqury | assembly statistics calculation | Rhie et al., 2020 |
| ToolName | Comments | Reference |
|---|---|---|
| RepeatMasker | masking/annotating repeats; Repbase needed | Smit, et al., 2015 |
| EDTA | repeat annotation | Ou et al., 2019 |
| panEDTA | pangenome repeat annotation | Ou et al., 2022 |
| ToolName | Comments | Reference |
|---|---|---|
| STAR | RNA-seq read mapping | Dobin et al., 2013 |
| HISAT2 | RNA-seq read mapping | Kim et al., 2019 |
| minimap2 | long read mapping | Li, 2018 |
| ToolName | Comments | Reference |
|---|---|---|
| BWA MEM | short read mapping | Li, 2013 |
| GATK | short read variant calling | Van der Auwera GA & O'Connor BD., 2020 |
| SVIM2 | long read variant calling | Heller & Vingron, 2019 |
| Sniffles2 | long read variant calling | Smolka et al., 2024 |
| SnpEff | variant impact prediction | Cingolani et al., 2012 |
| NAVIP | variant impact prediction | Baasner et al., 2019 |
| ToolName | Comments | Reference |
|---|---|---|
| BRAKER3 | protein coding gene prediction | Gabriel et al., 2023 |
| Augustus | protein coding gene prediction | Stanke et al., 2006 |
| GeMoMa | protein coding gene prediction | Keilwagen et al., 2019 |
| TSEBRA | merge annotations | Gabriel et al., 2021 |
| tRNAscan-SE | tRNAs, rRNAs | Chan et al., 2021 |
| BUSCO | assembly/annotation completeness check | Manni et al., 2021 |
| ToolName | Comments | Reference |
|---|---|---|
| MCscan | synteny analysis | Wang et al., 2012 |
| TBtools-II | comparative genomics | Chen et al,. 2023 |
| TOGA | synteny analysis | Kirilenko et al., 2023 |
| ToolName | Comments | Reference |
|---|---|---|
| InterProScan5 | universal functional annotation | Jones et al., 2014 |
| KIPEs | biosynthesis pathway annotation | Rempel et al., 2023 |
| MYB_annotator | R2R3-MYB annotation | Pucker, 2022 |
| bHLH_annotator | bHLH annotation | Thoben & Pucker, 2023 |
| Mercator | universal functional annotation | Lohse et al., 2014 |
| BLAST2GO | universal functional annotation | Conesa et al., 2005 |
| KEGG Mapper | KEGG ID assignment | Kanehisa & Sato, 2020 |
| BLAST | sequence comparison | Altschul et al., 1990 |
| DIAMOND | Buchfink et al., 2015 | |
| HMMER | sequence comparison | Finn et al., 2011 |
| KAAS | assigning KEGG IDs | Moriya et al., 2007 |
| ENTAP | - | Hart et al., 2019 |
| eggNOG-mapper | assigning eggNOG IDs | Cantalapiedra et al., 2021 |
| ToolName | Comments | Reference |
|---|---|---|
| fastq-dump | FASTQ downloads | NCBI |
| kallisto | gene expression quantification | Bray et al., 2016 |
| WGCNA | coexpression analysis | Langfelder & Horvath, 2008 |
| GENIE3 | coexpression analysis | Huynh-Thu et al., 2010 |
| dynGENIE3 | coexpression analysis | Huynh-Thu & Geurts, 2018 |
| ToolName | Comments | Reference |
|---|---|---|
| MAFFT | multiple sequence alignment | Katoh & Standley, 2013 |
| MUSCLE | multiple sequence alignment | Edgar, 2022 |
| IQ-TREE2 | phylogenetic tree construction | Minh et al., 2020 |
| FastTree | phylogenetic tree construction | Price et al., 2010 |
| RAxML-NG | phylogenetic tree construction | Kozlov et al., 2019 |
| SHOOT | phylogenetic placement of sequence | Emms & Kelly, 2022 |
| iTOL | phylogenetic tree visualization | Letunic & Bork, 2021 |
| JustOrthologs | ortholog identification | Miller et al., 2019 |
| SwiftOrtho | ortholog identification | Hu & Friedberg, 2019 |
| FastOMA | ortholog identification | Majidian et al., 2024 |
| ToolName | Comments | Reference |
|---|---|---|
| jbrowse | genome browser | Diesh et al., 2023 |
| gbrowse | genome browser | Stein, 2013 |
| Phytozome | plant genome database | Goodstein et al., 2012 |
| JGI Plant Gene Atlas | gene expression atlas | Sreedasyam et al., 2023 |
| SRA | sequencing database | NCBI |
| GEO | gene expression database | NCBI |
| OrthoDB | ortholog database | Kuznetsov et al., 2022 |
| ToolName | Comments | Reference |
|---|---|---|
| TAIR | Arabidopsis database | Berardini et al., 2015 |
| Banana Genome Hub | Musa database | Droc et al., 2022 |
| Coffee Genome Hub | Coffea database | Dereeper et al., 2015 |
| Sol Genomics Network | Solanaceae database | Fernandez-Pozo et al., 2014 |
| Cassava Genome Hub | Cassava database | (offline?) |
| Cocoa Genome Hub | Cacao database | Argout et al., 2017 |
| Grass Genome Hub | Grass database | website |
| Rice Genome Hub | Rice database | website |
| Sugarcane Genome Hub | Sugarcane database | Garsmeur et al., 2018 |
There are also specific collection of tools for particular purposes:
If you have questions about plant genomics that were not answered by any of these resources, please feel free to get in touch with the Plant Biotechnology and Biotechnology research group at TU Braunschweig.