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Hosting git repositories -- Gitolite allows you to setup git hosting on a central server, with very fine-grained access control and many (many!) more powerful features.
a tool for backing up your data using rsync (if you want to get help, use https://lists.sourceforge.net/lists/listinfo/rsnapshot-discuss)
ggplot2: elegant graphics for data analysis
DuckDuckGo Instant Answers based on Perl & JavaScript
✂️ ⚡ Rapid haploid variant calling and core genome alignment
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…
💾 📃 "Reads to report" for public health and clinical microbiology
🐉 🪰 Assemble bacterial isolate genomes from Nanopore reads
Phylogenetic and taxonomic analysis for genomes and metagenomes
Bioinformatics scripts produced over the course of my work. Now maintained on GitLab.
Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniP…
Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a QC step (NO LONGER MANTAINED)
starfish: a modular toolkit for giant mobile element annotation
A toolkit for annotation of transposable element families from unassembled sequence reads
Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
(a) (p)erfect (c)ircle? ... tests DNA sequences for overlapping ends, then trims and rejoins, and aligns reads to test the join