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New and updated tools 2025-12-10 #377

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42 changes: 42 additions & 0 deletions _posts/2025-12-10-tool-updates.md
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Original file line number Diff line number Diff line change
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---
site: freiburg
title: 'Galaxy Australia tool updates 2025-12-10'
tags: [tools]
supporters:
- galaxyaustralia
- melbinfo
- qcif
---


<style>
table {
width: 100%;
margin: 10px 20px;
}
table th {
display: none;
}
td {
padding: 3px 5px;
}
tr td:nth-child(1) {
vertical-align: top;
width: 25%;
}
</style>

### Tools updated

| Section | Tool |
|---------|-----|
| **Assembly** | genomescope [0bace381c9fd](https://toolshed.g2.bx.psu.edu/view/iuc/genomescope/0bace381c9fd) |
| **Convert Formats** | samtools_bam_to_cram [3a2d8de89c73](https://toolshed.g2.bx.psu.edu/view/iuc/samtools_bam_to_cram/3a2d8de89c73) |
| **FASTA/FASTQ** | fastq_filter [ff7d49ec777f](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_filter/ff7d49ec777f)<br/>fastq_groomer [10d4df6a9d94](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_groomer/10d4df6a9d94)<br/>fastq_manipulation [e06d41f3ed3e](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_manipulation/e06d41f3ed3e)<br/>fastq_paired_end_deinterlacer [c48cf4699be7](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_deinterlacer/c48cf4699be7)<br/>fastq_paired_end_interlacer [acb5090e281f](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_interlacer/acb5090e281f)<br/>fastq_paired_end_joiner [115f6bb3ae79](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_joiner/115f6bb3ae79)<br/>fastq_paired_end_splitter [7fafac615aa1](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_paired_end_splitter/7fafac615aa1)<br/>fastqtofasta [4a3e93647a4e](https://toolshed.g2.bx.psu.edu/view/devteam/fastqtofasta/4a3e93647a4e)<br/>fastq_trimmer [fe86fb89562d](https://toolshed.g2.bx.psu.edu/view/devteam/fastq_trimmer/fe86fb89562d)<br/>seqkit_sort [9ba18868a990](https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_sort/9ba18868a990)<br/>seqkit_stats [24107542edff](https://toolshed.g2.bx.psu.edu/view/iuc/seqkit_stats/24107542edff) |
| **Graph/Display Data** | volcanoplot [e4790edb4299](https://toolshed.g2.bx.psu.edu/view/iuc/volcanoplot/e4790edb4299) |
| **Metagenomic Analysis** | metawrapmg_binning [cbd58ca70eac](https://toolshed.g2.bx.psu.edu/view/galaxy-australia/metawrapmg_binning/cbd58ca70eac)<br/>semibin_generate_cannot_links [fd17362def4f](https://toolshed.g2.bx.psu.edu/view/iuc/semibin_generate_cannot_links/fd17362def4f) |
| **Multiple Alignments** | trimal [c2008ab22c09](https://toolshed.g2.bx.psu.edu/view/iuc/trimal/c2008ab22c09) |
| **Nanopore** | medaka_consensus [fc1f197b33ec](https://toolshed.g2.bx.psu.edu/view/iuc/medaka_consensus/fc1f197b33ec)<br/>medaka_consensus_pipeline [d9b6a4615626](https://toolshed.g2.bx.psu.edu/view/iuc/medaka_consensus_pipeline/d9b6a4615626)<br/>nanoplot [9eab750c367d](https://toolshed.g2.bx.psu.edu/view/iuc/nanoplot/9eab750c367d) |
| **SAM/BAM** | mosdepth [2fe966f8532e](https://toolshed.g2.bx.psu.edu/view/iuc/mosdepth/2fe966f8532e)<br/>samtools_fixmate [68a116f469db](https://toolshed.g2.bx.psu.edu/view/iuc/samtools_fixmate/68a116f469db)<br/>samtools_view [5ec526530725](https://toolshed.g2.bx.psu.edu/view/iuc/samtools_view/5ec526530725) |
| **Single-cell** | scanpy_cluster_reduce_dimension [49ce1315722c](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_cluster_reduce_dimension/49ce1315722c)<br/>scanpy_inspect [27c054e8d949](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_inspect/27c054e8d949)<br/>scanpy_plot [16a1c3122996](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_plot/16a1c3122996)<br/>scanpy_remove_confounders [be0d45c46e97](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/be0d45c46e97)<br/>snapatac2_clustering [d258720d9a42](https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_clustering/d258720d9a42)<br/>snapatac2_peaks_and_motif [02a7162fc510](https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_peaks_and_motif/02a7162fc510)<br/>snapatac2_preprocessing [20c4011e1458](https://toolshed.g2.bx.psu.edu/view/iuc/snapatac2_preprocessing/20c4011e1458) |
| **VCF/BCF** | bcftools_annotate [06eaadeffb7d](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_annotate/06eaadeffb7d)<br/>bcftools_call [c277260d3fab](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_call/c277260d3fab)<br/>bcftools_cnv [61dfbc82ffc8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_cnv/61dfbc82ffc8)<br/>bcftools_concat [c3c930926708](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_concat/c3c930926708)<br/>bcftools_convert_from_vcf [a20d6492132d](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_convert_from_vcf/a20d6492132d)<br/>bcftools_filter [3502f0e1f0e4](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_filter/3502f0e1f0e4)<br/>bcftools_gtcheck [68d04cd5d35a](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_gtcheck/68d04cd5d35a)<br/>bcftools_isec [3d21f507fc5d](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_isec/3d21f507fc5d)<br/>bcftools_merge [d3286f971e89](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_merge/d3286f971e89)<br/>bcftools_plugin_counts [ade0d3c3ec1c](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_counts/ade0d3c3ec1c)<br/>bcftools_plugin_dosage [0c50683a9c94](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_dosage/0c50683a9c94)<br/>bcftools_plugin_fill_an_ac [69ad30be1a8b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_an_ac/69ad30be1a8b)<br/>bcftools_plugin_fill_tags [fea209b23f19](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fill_tags/fea209b23f19)<br/>bcftools_plugin_fixploidy [f203ea355bc8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_fixploidy/f203ea355bc8)<br/>bcftools_plugin_impute_info [42345cc2c76e](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_impute_info/42345cc2c76e)<br/>bcftools_plugin_mendelian [eed37e76acd1](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_mendelian/eed37e76acd1)<br/>bcftools_plugin_missing2ref [793ae03deb13](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_missing2ref/793ae03deb13)<br/>bcftools_plugin_setgt [394dbf428c7b](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_setgt/394dbf428c7b)<br/>bcftools_plugin_tag2tag [9268b0ad92af](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_plugin_tag2tag/9268b0ad92af)<br/>bcftools_query [1dc6f1ac7f32](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query/1dc6f1ac7f32)<br/>bcftools_query_list_samples [fb631fd605e8](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_query_list_samples/fb631fd605e8)<br/>bcftools_reheader [a0b1c0bdfa5a](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_reheader/a0b1c0bdfa5a)<br/>bcftools_roh [acfd6984d130](https://toolshed.g2.bx.psu.edu/view/iuc/bcftools_roh/acfd6984d130) |