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saffrontreeSaffronTree: Reference free rapid phylogenetic tree construction from raw read data
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gubbinsRapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
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catchA package for designing compact and comprehensive capture probe sets.
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GalaxyData intensive science for everyone.
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SequenceserverIntuitive local web frontend for the BLAST bioinformatics tool
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SnsAnalysis pipelines for sequencing data
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snp-sitesFinds SNP sites from a multi-FASTA alignment file
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Fastq.bioAn interactive web tool for quality control of DNA sequencing data
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assembly improvementImprove the quality of a denovo assembly by scaffolding and gap filling
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tiptoftPredict plasmids from uncorrected long read data
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PygenoPersonalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
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PostguiA React web application to query and share any PostgreSQL database.
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Vcfannoannotate a VCF with other VCFs/BEDs/tabixed files
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PyfaidxEfficient pythonic random access to fasta subsequences
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JvarkitJava utilities for Bioinformatics
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CoolerA cool place to store your Hi-C
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Bio.jl[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
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Gwa tutorialA comprehensive tutorial about GWAS and PRS
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Bwa Mem2The next version of bwa-mem
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UgeneUGENE is free open-source cross-platform bioinformatics software
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DeeptoolsTools to process and analyze deep sequencing data.
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JcviPython library to facilitate genome assembly, annotation, and comparative genomics
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HailScalable genomic data analysis.
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Helmsmanhighly-efficient & lightweight mutation signature matrix aggregation
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JbrowseA modern genome browser built with JavaScript and HTML5.
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FastpAn ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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BwaBurrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
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BgtFlexible genotype query among 30,000+ samples whole-genome
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Tiledb VcfEfficient variant-call data storage and retrieval library using the TileDB storage library.
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