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panaroo_combine_gene_aln Public
Panaroo standalone script to combine aligned genes
Python Other UpdatedMar 17, 2025 -
itolparser Public
Small script to produce iTOL colorstrip metadata files from a table
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distle Public
Forked from KHajji/distleFast distance matrix calculations on fasta and cgmlst files
Rust GNU General Public License v3.0 UpdatedAug 22, 2024 -
abricate_ecoli_K_typing Public
ABRicate database to identify K1, K2 and K5 genes in Escherichia coli WGS data
JavaScript UpdatedAug 22, 2024 -
assembly_snptyper Public
Type assembly based on a VCF using minimap2 + samtools
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bioconda-recipes Public
Forked from bioconda/bioconda-recipesConda recipes for the bioconda channel.
Shell MIT License UpdatedJun 25, 2024 -
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snp-dists Public
Forked from tseemann/snp-distsPairwise SNP distance matrix from a FASTA sequence alignment
C GNU General Public License v3.0 UpdatedMar 6, 2024 -
juno-assembly Public
Forked from RIVM-bioinformatics/juno-assemblyPipeline to process raw sequencing data up to de-novo assembly and the accompanying statistics
Python GNU Affero General Public License v3.0 UpdatedNov 13, 2023 -
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extract_genes_ABRicate Public
Small script to use ABRicate output to extract genes from genome assemblies, reverse complement if necessary, and print to a file
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nanopore_methylation_R9 Public
(Pseudo)code for ONT de novo methylation analysis
UpdatedJun 16, 2023 -
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GAS_M4 Public
Snakemake pipeline to analyse genomic data of Streptococcus pyogenes M4
Python UpdatedDec 23, 2022 -
pyelonephritis Public
Snakemake pipeline to link urine metagenomic sequencing data from pyelonephritis patients to cultured sepsis isolates
Python UpdatedAug 8, 2022 -
MRA_Streptococcus_suis Public
Repository for the Microbiology Resource Announcements paper on five complete Streptococcus suis genomes
Python UpdatedAug 2, 2022 -
ABRicate_to_prokka Public
Match ABRicate hits to Prokka locus tags based on contig names and locations
Python MIT License UpdatedApr 12, 2022 -
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PIRATE Public
Forked from SionBayliss/PIRATEA toolbox for pangenome analysis and threshold evaluation.
Perl GNU General Public License v3.0 UpdatedJul 12, 2021 -
abricate Public
Forked from tseemann/abricate🔎 💊 Mass screening of contigs for antimicrobial and virulence genes
Perl GNU General Public License v2.0 UpdatedJul 2, 2021 -
pacbio_methylation_snakemake Public
Small pipeline to call methylation in Streptococcus suis using standard PacBio tools
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mlst_to_phyloviz Public
Small script to convert output from tseemann/mlst to allelic profile data for PhyloViz, with some extra checks
Python UpdatedJun 17, 2021 -
Scripts to match chewBBACA output to Enterobase cgMLST and hierarchical CCs
Python MIT License UpdatedMay 16, 2021 -
submission_checklist Public
Forked from philippbayer/submission_checklistMIT License UpdatedMay 3, 2021 -
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