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brewsci / homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
http://brewsci.github.io/homebrew-bio
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Updates #1

Open sjackman opened 6 years ago

sjackman commented 6 years ago

Subscribe to this issue to receive updates about Brewsci/bio.

tseemann commented 6 years ago

🎉 New formula kent-tools in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/kent-tools 🏠 https://genome.ucsc.edu/

sjackman commented 6 years ago

🎉 New formula porechop in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/porechop 🏡 https://github.com/rrwick/Porechop

sjackman commented 6 years ago

🎉 New formula unicycler in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/unicycler 🏡 https://github.com/rrwick/Unicycler 📖 https://doi.org/10.1371/journal.pcbi.1005595

sjackman commented 6 years ago

🎉 New formula circos in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/circos 🏠 http://circos.ca 📖 https://doi.org/10.1101/gr.092759.109

sjackman commented 6 years ago

🎉 New formula artemis in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/artemis 🏠 https://www.sanger.ac.uk/science/tools/artemis 📖 https://doi.org/10.1093/bioinformatics/btr703

sjackman commented 6 years ago

🎉 New formula transdecoder in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/transdecoder 🏠 https://transdecoder.github.io/

sjackman commented 6 years ago

🎉 New formula meme in Brewsci/bio for Linux! đŸē brew install brewsci/bio/meme 🏠 http://meme-suite.org 📖 https://doi.org/10.1093/nar/gkp335

sjackman commented 6 years ago

🎉 New formula exonerate in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/exonerate 🏠 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 📖 https://doi.org/10.1186/1471-2105-6-31

sjackman commented 6 years ago

🎉 New formula snoscan in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/snoscan 🏠 http://lowelab.ucsc.edu/snoscan/ 📖 https://doi.org/10.1126/science.283.5405.1168

sjackman commented 6 years ago

🎉 New formula trnascan in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/trnascan 🏡 http://eddylab.org/software.html 📖 https://doi.org/10.1093/nar/25.5.0955

sjackman commented 6 years ago

🎉 New formula e-mem in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/e-mem 🏡 https://www.csd.uwo.ca/~ilie/E-MEM/ 📖 https://doi.org/10.1093/bioinformatics/btu687

sjackman commented 6 years ago

🎉 New formula matplotlib in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/matplotlib 🏠 https://matplotlib.org

sjackman commented 6 years ago

🎉 New formula seqkit in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/seqkit 🏠 https://bioinf.shenwei.me/seqkit/

sjackman commented 6 years ago

🎉 New formula viennarna in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/viennarna 🏠 https://www.tbi.univie.ac.at/~ronny/RNA/ 📖 https://doi.org/10.1186/1748-7188-6-26

sjackman commented 6 years ago

🎉 New formula genewise in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/genewise 🏠 https://www.ebi.ac.uk/~birney/wise2/ 📖 https://doi.org/10.1101/gr.1865504

sjackman commented 6 years ago

🎉 New formula mir-prefer in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/mir-prefer 🏠 https://github.com/hangelwen/miR-PREFeR 📖 https://doi.org/10.1093/bioinformatics/btu380

tseemann commented 6 years ago

🎉 New formula mlst in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/mlst 🏠 https://github.com/tseemann/mlst

tseemann commented 6 years ago

🎉 New formula art in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/art 🏠 https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm 📖 https://doi.org/10.1093/bioinformatics/btr708

tseemann commented 6 years ago

🎉 New formula muscle in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/muscle 🏠 https://www.drive5.com/muscle/ 📖 https://doi.org/10.1186/1471-2105-5-113

tseemann commented 6 years ago

🎉 New formula minimap in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/minimap 🏠 https://github.com/lh3/minimap

tseemann commented 6 years ago

🎉 New formula mcl in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/mcl 🏠 https://micans.org/mcl 📖 https://doi.org/10.1093/nar/30.7.1575

sjackman commented 6 years ago

🎉 New formula quast in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/quast 🏠 http://cab.spbu.ru/software/quast/ 📖 https://doi.org/10.1093/bioinformatics/btw379

tseemann commented 6 years ago

🎉 New formula newick-utils in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/newick-utils 🏠 http://cegg.unige.ch/newick_utils :book: https://doi.org/10.1093/bioinformatics/btq243

tseemann commented 6 years ago

🎉 New formula minia in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/minia 🏠 http://minia.genouest.org/ 📖 https://doi.org/10.1186/1748-7188-8-22

tseemann commented 6 years ago

🎉 New formula hmmer2 in Brewsci/bio for Linux! đŸē brew install brewsci/bio/hmmer2 🏠 http://hmmer.org/ 📖 https://doi.org/10.1142/9781848165632_0019 📖 https://doi.org/10.1186/1471-2105-11-431 📖 https://doi.org/10.1371/journal.pcbi.1002195

tseemann commented 6 years ago

🎉 New formula mhap in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/mhap 🏠 https://github.com/marbl/MHAP 📖 https://doi.org/10.1038/nbt.3238

sjackman commented 6 years ago

🎉 New formula bioperl in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/bioperl 🏡 http://bioperl.org 📖 https://doi.org/10.1101/gr.361602

tseemann commented 6 years ago

🎉 New formula quicktree in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/quicktree 🏠 https://www.sanger.ac.uk/science/tools/quicktree

tseemann commented 6 years ago

🎉 New formula clustal-w in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/clustal-w 🏠 http://www.clustal.org/clustal2/ 📖 https://doi.org/10.1093/bioinformatics/btm404

tseemann commented 6 years ago

🎉 New formula clustal-omega in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/clustal-omega 🏠 http://www.clustal.org/omega/

tseemann commented 6 years ago

🎉 New formula rapidnj in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/rapidnj 🏠 https://birc.au.dk/Software/RapidNJ/ 📖 https://doi.org/10.1007/978-3-540-87361-7_10

sjackman commented 6 years ago

🎉 New formula kat in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/kat 🏡 https://github.com/TGAC/KAT 📖 https://doi.org/10.1093/bioinformatics/btw663

sjackman commented 6 years ago

🎉 New formula maker in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/maker 🏡 http://www.yandell-lab.org/software/maker.html 📖 http://doi.org/10.1101/gr.6743907 📖 http://doi.org/10.1186/1471-2105-12-491 📖 http://doi.org/10.1104/pp.113.230144

tseemann commented 6 years ago

🎉 New formula emboss in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/emboss 🏠 https://emboss.sourceforge.io/ 📖 http://doi.org/10.1016/S0168-9525(00)02024-2

tseemann commented 6 years ago

🎉 New formula velvet in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/velvet 🏠 https://www.ebi.ac.uk/~zerbino/velvet/ 📖 https://doi.org/10.1101/gr.074492.107

tseemann commented 6 years ago

🎉 New formula velvetoptimiser in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/velvetoptimiser 🏠 https://github.com/tseemann/VelvetOptimiser

tseemann commented 6 years ago

🎉 New formula oases in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/oases 🏠 https://www.ebi.ac.uk/~zerbino/oases/ 📖 https://doi.org/10.1093/bioinformatics/bts094

tseemann commented 6 years ago

🎉 New formula rapidnj in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/rapidnj 🏠 https://birc.au.dk/Software/RapidNJ/ 📖 https://doi.org/10.1007/978-3-540-87361-7_10

tseemann commented 6 years ago

🎉 New formula varsim in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/varsim 🏠 https://github.com/bioinform/varsim

tseemann commented 6 years ago

🎉 New formula abacas in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/abacas 🏠 https://abacas.sourceforge.io 📖 https://doi.org/10.1093/bioinformatics/btp347

tseemann commented 6 years ago

🎉 New formula varscan in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/varscan 🏠 https://dkoboldt.github.io/varscan/ 📖 https://doi.org/10.1101/gr.129684.111

tseemann commented 6 years ago

🎉 New formula readseq in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/readseq 🏠 http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

tseemann commented 6 years ago

🎉 New formula abricate in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/abricate 🏠 https://github.com/tseemann/abricate

tseemann commented 6 years ago

🎉 New formula kraken in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/kraken 🏠 https://ccb.jhu.edu/software/kraken/ 📖 https://doi.org/10.1186/gb-2014-15-3-r46

tseemann commented 6 years ago

🎉 New formula vt in Brewsci/bio for Linux and MacOS! đŸē brew install brewsci/bio/vt 🏠 https://genome.sph.umich.edu/wiki/Vt

jonchang commented 6 years ago

🎉 New formula treepl in Brewsci/bio for Linux and macOS! ℹī¸ Dating phylogenies with penalized likelihood đŸē brew install brewsci/bio/treepl 🏡 https://github.com/blackrim/treePL/wiki 📖 https://doi.org/10.1093/bioinformatics/bts492

tseemann commented 6 years ago

🎉 New formula paml in Brewsci/bio for Linux and macOS! ℹī¸ Phylogenetic analysis by maximum likelihood đŸē brew install brewsci/bio/paml 🏡 http://abacus.gene.ucl.ac.uk/software/paml.html 📖 https://doi.org/10.1093/molbev/msm088

tseemann commented 6 years ago

🎉 New formula cannoli in Brewsci/bio for Linux and macOS! ℹī¸ Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools đŸē brew install brewsci/bio/cannoli 🏡 https://github.com/bigdatagenomics/cannoli

sjackman commented 6 years ago

🎉 New formula bowtie in Brewsci/bio for Linux and macOS! ℹī¸ Ultrafast memory-efficient short read aligner đŸē brew install brewsci/bio/bowtie 🏡 https://bowtie-bio.sourceforge.io/ 📖 https://doi.org/10.1186/gb-2009-10-3-r25

sjackman commented 6 years ago

🎉 New formula nonpareil in Brewsci/bio for Linux and macOS! ℹī¸ Estimates coverage in metagenomic datasets đŸē brew install brewsci/bio/nonpareil 🏡 http://enve-omics.ce.gatech.edu/nonpareil 📖 https://doi.org/10.1093/bioinformatics/btt584