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fetch all tools bot - step filter
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<td>(3/3)</td>
<td>(1/3)</td>
</tr>
<tr>
<td></td>
<td>tiara</td>
<td></td>
<td></td>
<td>tiara</td>
<td>Tool for identification of eukaryotic sequences in the metagenomic datasets.</td>
<td>Tiara</td>
<td>Tiara</td>
<td></td>
<td>TIARA</td>
<td>Total Integrated Archive of Short-Read and Array (TIARA) database, contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs).</td>
<td>Genome comparison, Data retrieval, Variant calling, Genome visualisation, Structural variation detection</td>
<td>Sequencing, Genomics, DNA polymorphism, DNA structural variation</td>
<td>To update</td>
<td>https://github.com/ibe-uw/tiara</td>
<td>Metagenomics, Sequence Analysis</td>
<td>tiara</td>
<td>bgruening</td>
<td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
<td>https://github.com/bgruening/galaxytools/tree/master/tools/tiara</td>
<td>1.0.3</td>
<td>tiara</td>
<td></td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
</tr>
<tr>
<td></td>
<td>trim_galore</td>
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<td>AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search "plus", stress, heat, and biocide resistance and virulence factors for some organisms</td>
<td>Antimicrobial resistance prediction</td>
<td>Microbiology, Public health and epidemiology, Infectious disease</td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/ncbi/amr</td>
<td>Sequence Analysis</td>
<td>AMRFinderPlus</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/amrfinderplus</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus</td>
<td>3.11.26</td>
<td>3.12.8</td>
<td>ncbi-amrfinderplus</td>
<td>3.12.8</td>
<td>(0/1)</td>
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<td>151.0</td>
<td>bakta</td>
<td>"Bakta is a tool for the rapid &amp; standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON &amp; bioinformatics standard file formats for automatic downstream analysis."</td>
<td>Bakta</td>
<td>Bakta</td>
<td>bakta</td>
<td>bakta</td>
<td></td>
<td>Bakta</td>
<td>Rapid &amp; standardized annotation of bacterial genomes, MAGs &amp; plasmids</td>
<td>Genome annotation</td>
<td>Genomics, Data submission, annotation and curation, Sequence analysis</td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/oschwengers/bakta</td>
<td>Sequence Analysis</td>
<td>bakta</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/bakta</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta</td>
<td>1.9.2</td>
<td>1.9.3</td>
<td>bakta</td>
<td>1.9.3</td>
<td>(0/1)</td>
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<td>(5/5)</td>
<td>(5/5)</td>
</tr>
<tr>
<td></td>
<td>cosg</td>
<td></td>
<td></td>
<td>cosg</td>
<td>Marker gene identification for single-cell sequencing data using COSG.</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td>Up-to-date</td>
<td>https://github.com/genecell/COSG</td>
<td>Transcriptomics, Sequence Analysis</td>
<td>cosg</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg</td>
<td>1.0.1</td>
<td>cosg</td>
<td>1.0.1</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
</tr>
<tr>
<td></td>
<td>coverm</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy</td>
<td>2.5.47</td>
<td>hyphy</td>
<td>2.5.61</td>
<td>2.5.62</td>
<td>(17/17)</td>
<td>(2/17)</td>
<td>(17/17)</td>
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<td>A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time</td>
<td>Phylogenetic analysis, Sequence analysis</td>
<td>Phylogenetics</td>
<td>To update</td>
<td>Up-to-date</td>
<td>http://www.iqtree.org/</td>
<td>Phylogenetics</td>
<td>iqtree</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree</td>
<td>2.3.3</td>
<td>2.3.4</td>
<td>iqtree</td>
<td>2.3.4</td>
<td>(1/1)</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan</td>
<td>4.0.6</td>
<td>metaphlan</td>
<td>4.1.0</td>
<td>4.1.1</td>
<td>(1/4)</td>
<td>(2/4)</td>
<td>(4/4)</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc</td>
<td>1.11</td>
<td>multiqc</td>
<td>1.22.1</td>
<td>1.22.2</td>
<td>(1/1)</td>
<td>(1/1)</td>
<td>(1/1)</td>
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<td></td>
<td>ncbi_fcs_gx</td>
<td>FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX).</td>
<td>ncbi_fcs</td>
<td>ncbi_fcs</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td>NCBI fcs</td>
<td>The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank.</td>
<td>Sequence assembly validation, Sequence trimming, Sequence contamination filtering</td>
<td>Sequence analysis, Sequence assembly</td>
<td>Up-to-date</td>
<td>https://github.com/ncbi/fcs-gx</td>
<td>Sequence Analysis</td>
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<td>FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations.</td>
<td>DNA transcription, Sequence trimming, DNA translation, Sequence conversion</td>
<td>Database management, Sequence analysis</td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://bioinf.shenwei.me/seqkit/</td>
<td>Sequence Analysis</td>
<td>seqkit</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit</td>
<td>2.8.1</td>
<td>2.8.2</td>
<td>seqkit</td>
<td>2.8.2</td>
<td>(0/5)</td>
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<td>Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations.</td>
<td>Read pre-processing, Sequence alignment, Genetic variation analysis</td>
<td>Genomics, Population genetics, Workflows, Virology, Sequencing</td>
<td>Up-to-date</td>
<td>To update</td>
<td>https://github.com/cbg-ethz/smallgenomeutilities</td>
<td>Sequence Analysis</td>
<td>smallgenomeutilities</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities</td>
<td>0.4.0</td>
<td>smallgenomeutilities</td>
<td>0.4.0</td>
<td>0.4.1</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(1/1)</td>
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<td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
<td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
<td>spades</td>
<td>biosyntheticspades, coronaspades, plasmidspades, rnaspades, rnaviralspades, metaspades, metaplasmidspades, spades, metaviralspades</td>
<td>rnaspades, biosyntheticspades, spades, plasmidspades, metaplasmidspades, rnaviralspades, coronaspades, metaviralspades, metaspades</td>
<td></td>
<td>SPAdes</td>
<td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
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<td>A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants).</td>
<td>Antimicrobial resistance prediction</td>
<td></td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/jodyphelan/TBProfiler</td>
<td>Sequence Analysis</td>
<td>tbprofiler</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler</td>
<td>4.4.1</td>
<td>6.2.1</td>
<td>tb-profiler</td>
<td>6.2.1</td>
<td>(1/1)</td>
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<td></td>
<td></td>
<td></td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/jonas-fuchs/virHEAT</td>
<td>Visualization, Variant Analysis</td>
<td>virheat</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat</td>
<td>0.6</td>
<td>0.7</td>
<td>virheat</td>
<td>0.7</td>
<td>(0/1)</td>
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<td>(16/18)</td>
<td>(16/18)</td>
</tr>
<tr>
<td></td>
<td>frogs</td>
<td></td>
<td></td>
<td>FROGS_affiliation_filters, FROGS_affiliation_postprocess, FROGS_affiliation_stats, FROGS_biom_to_stdBiom, FROGS_biom_to_tsv, FROGS_cluster_filters, FROGS_cluster_stats, FROGS_clustering, FROGS_demultiplex, FROGSSTAT_DESeq2_Preprocess, FROGSSTAT_DESeq2_Visualisation, FROGSFUNC_step2_functions, FROGSFUNC_step3_pathways, FROGSFUNC_step1_placeseqs, FROGS_itsx, FROGS_normalisation, FROGSSTAT_Phyloseq_Alpha_Diversity, FROGSSTAT_Phyloseq_Beta_Diversity, FROGSSTAT_Phyloseq_Sample_Clustering, FROGSSTAT_Phyloseq_Composition_Visualisation, FROGSSTAT_Phyloseq_Import_Data, FROGSSTAT_Phyloseq_Multivariate_Analysis_Of_Variance, FROGSSTAT_Phyloseq_Structure_Visualisation, FROGS_preprocess, FROGS_remove_chimera, FROGS_taxonomic_affiliation, FROGS_Tree, FROGS_tsv_to_biom</td>
<td>Suite for metabarcoding analysis</td>
<td>frogs</td>
<td>frogs</td>
<td></td>
<td>FROGS</td>
<td>The user-friendly and Galaxy-supported pipeline FROGS analyses large sets of DNA amplicons sequences accurately and rapidly, essential for microbe community studies.</td>
<td>Taxonomic classification</td>
<td>Metagenomics, Microbial ecology, Taxonomy, Evolutionary biology, Sequencing</td>
<td>Up-to-date</td>
<td>http://frogs.toulouse.inrae.fr/</td>
<td>Metagenomics</td>
<td>frogs</td>
<td>frogs</td>
<td>https://github.com/geraldinepascal/FROGS-wrappers/</td>
<td>https://github.com/geraldinepascal/FROGS-wrappers/tree/master/tools/frogs</td>
<td>4.1.0</td>
<td>frogs</td>
<td>4.1.0</td>
<td>(0/28)</td>
<td>(0/28)</td>
<td>(0/28)</td>
<td>(28/28)</td>
</tr>
<tr>
<td></td>
<td>suite_qiime2__alignment</td>
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