Updates

[sjackman]

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

[sjackman]

🎉 New formula arcs in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/arcs
🏡 https://github.com/bcgsc/arcs
📖 https://doi.org/10.1093/bioinformatics/btx675

[sjackman]

🎉 New formula minimap2 in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/minimap2
🏡 https://github.com/lh3/minimap2
📖 https://arxiv.org/abs/1708.01492

[sjackman]

🎉 New formula fastani in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/fastani
🏡 https://github.com/ParBLiSS/FastANI
📖 https://doi.org/10.1101/225342

[sjackman]

🎉 New formula tbl2asn in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/tbl2asn
🏡 https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/

[sjackman]

🎉 New formula miniasm in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/miniasm
🏡 https://github.com/lh3/miniasm
📖 https://doi.org/10.1093/bioinformatics/btw152

[sjackman]

🎉 New formula canu in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/canu
🏡 https://canu.readthedocs.io/
📖 https://doi.org/10.1101/gr.215087.116

[sjackman]

🎉 New formula busco in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/busco
🏡 http://busco.ezlab.org
📖 https://doi.org/10.1093/bioinformatics/btv351

[sjackman]

🎉 New formula gepard in Brewsci/bio for Linux and macOS!
🍺 brew install brewsci/bio/gepard
🏡 http://cube.univie.ac.at/gepard
📖 https://doi.org/10.1093/bioinformatics/btm039

[sjackman]

🎉 New formula gatk in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/gatk
🏠 https://software.broadinstitute.org/gatk/
📖 https://doi.org/10.1101/gr.107524.110

[sjackman]

🎉 New formula metaphlan in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/metaphlan
🏠 https://huttenhower.sph.harvard.edu/metaphlan
📖 https://doi.org/10.1038/nmeth.2066

[sjackman]

🎉 New formula fwdpp in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/fwdpp
🏠 https://molpopgen.github.io/fwdpp/
📖 https://doi.org/10.1534/genetics.114.165019

[sjackman]

🎉 New formula pathvisio in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/pathvisio
🏡 https://www.pathvisio.org/
📖 https://doi.org/10.1371/journal.pcbi.1004085

[sjackman]

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

[tseemann]

🎉 New formula ascp in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/ascp
🏠 https://asperasoft.com/

[tseemann]

🎉 New formula figtree in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/figtree
🏠 http://tree.bio.ed.ac.uk/software/figtree/

[tseemann]

🎉 New formula gepard in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/gepard
🏠 http://cube.univie.ac.at/gepard
📖 https://doi.org/10.1093/bioinformatics/btm039

[tseemann]

🎉 New formula blast-legacy in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/blast-legacy
📖 https://doi.org/10.1093/nar/25.17.3389

[tseemann]

🎉 New formula kr in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/kr
🏠 http://guanine.evolbio.mpg.de/cgi-bin/kr2/kr.cgi.pl

[tseemann]

🎉 New formula light-assembler in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/light-assembler
🏠 https://github.com/SaraEl-Metwally/LightAssembler
📖 https://doi.org/10.1093/bioinformatics/btw470

[tseemann]

🎉 New formula ispcr in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/ispcr
🏠 http://hgwdev.cse.ucsc.edu/~kent/src/

[tseemann]

🎉 New formula jspecies in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/jspecies
🏠 https://imedea.uib-csic.es/jspecies/index.html
📖 https://doi.org/10.1073/pnas.0906412106

[tseemann]

🎉 New formula lofreq in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/lofreq
🏠 https://csb5.github.io/lofreq/
📖 https://10.1093/nar/gks918

[tseemann]

🎉 New formula snp-dists in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/snp-dists
🏠 https://github.com/tseemann/snp-dists

[sjackman]

🎉 New formula nanopolish in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/nanopolish
🏠 https://github.com/jts/nanopolish
📖 https://doi.org/10.1038/nmeth.3444

[tseemann]

🎉 New formula trimmomatic in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/trimmomatic
🏠 http://www.usadellab.org/cms/?page=trimmomatic
📖 https://doi.org/10.1093/bioinformatics/btu170

[tseemann]

🎉 New formula panito in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/panito
🏠 https://github.com/sanger-pathogens/panito

[sjackman]

🎉 New formula salmon in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/salmon
🏠 https://github.com/COMBINE-lab/salmon
📖 https://doi.org/10.1038/nmeth.4197

[tseemann]

🎉 New formula gzstream in Brewsci/bio for Linux and MacOS!
🍺 brew install brewsci/bio/gzstream
🏠 https://www.cs.unc.edu/Research/compgeom/gzstream/

[sjackman]

🎉 New formula ntjoin in Brewsci/bio for Linux and macOS!
ℹ️ Genome assembly scaffolder using minimizer graphs
🍺 brew install brewsci/bio/ntjoin
🏡 https://github.com/bcgsc/ntJoin
📖 https://doi.org/10.1101/2020.01.13.905240

[sjackman]

🎉 New formula seqan@3 in Brewsci/bio for Linux and macOS!
ℹ️ The modern C++ library for sequence analysis
🍺 brew install brewsci/bio/seqan@3
🏡 https://www.seqan.de
📖 https://doi.org/10.1186/1471-2105-9-11

[sjackman]

🎉 New formula [email protected] in Brewsci/bio for Linux and macOS!
ℹ️ Basic Local Alignment Search Tool
🍺 brew install brewsci/bio/[email protected]
🏡 https://blast.ncbi.nlm.nih.gov/

[sjackman]

🎉 New formula souporcell in Brewsci/bio for Linux and macOS!
ℹ️ Clustering scRNAseq by genotypes
🍺 brew install brewsci/bio/souporcell
🏡 https://github.com/wheaton5/souporcell
📖 https://www.biorxiv.org/content/10.1101/699637v1

[sjackman]

🎉 New formula hh-suite in Brewsci/bio for Linux and macOS!
ℹ️ Remote protein homology detection suite
🍺 brew install brewsci/bio/hh-suite
🏡 https://github.com/soedinglab/hh-suite
📖 https://doi.org/10.1186/s12859-019-3019-7

[sjackman]

🎉 New formula r2r in Brewsci/bio for Linux and macOS!
ℹ️ Software to speed depiction of aesthetic consensus RNA secondary structures
🍺 brew install brewsci/bio/r2r
🏡 https://sourceforge.net/projects/weinberg-r2r
📖 https://doi.org/10.1186/1471-2105-12-3

[sjackman]

🎉 New formula bodr in Brewsci/bio for Linux and macOS!
ℹ️ Database of chemoinformatics
🍺 brew install brewsci/bio/bodr
🏡 https://www.sourceforge.net/projects/bodr

[sjackman]

🎉 New formula iqtree2 in Brewsci/bio for Linux and macOS!
ℹ️ Efficient phylogenomic software by maximum likelihood
🍺 brew install brewsci/bio/iqtree2
🏡 http://www.iqtree.org/
📖 https://doi.org/10.1093/molbev/msu300

[sjackman]

🎉 New formula raptor in Homebrew/core for Linux and macOS!
ℹ️ RDF parser toolkit
🍺 brew install raptor
🏡 http://librdf.org/raptor/

[sjackman]

🎉 New formula psmc in Brewsci/bio for Linux and macOS!
ℹ️ Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
🍺 brew install brewsci/bio/psmc
🏡 https://github.com/lh3/psmc
📖 https://doi.org/10.1038/nature10231

[sjackman]

🎉 New formula gffcompare in Brewsci/bio for Linux and macOS!
ℹ️ Classify, merge, tracking and annotation of GFF files
🍺 brew install brewsci/bio/gffcompare
🏡 https://github.com/gpertea/gffcompare

[sjackman]

🎉 New formula hssp in Brewsci/bio for Linux and macOS!
ℹ️ Create HSSP file
🍺 brew install brewsci/bio/hssp
🏡 https://github.com/cmbi/xssp
📖 https://doi.org/10.1093/nar/gku1028

[sjackman]

🎉 New formula dssp in Brewsci/bio for Linux and macOS!
ℹ️ Create DSSP files
🍺 brew install brewsci/bio/dssp
🏡 https://github.com/cmbi/dssp
📖 https://doi.org/10.1093/nar/gku1028

[sjackman]

🎉 New formula bmdca in Brewsci/bio for Linux and macOS!
ℹ️ Boltzmann-machine Direct Coupling Analysis
🍺 brew install brewsci/bio/bmdca
🏡 https://github.com/ranganathanlab/bmDCA/
📖 https://doi.org/10.1093/molbev/msy007

[sjackman]

🎉 New formula tmalign in Brewsci/bio for Linux and macOS!
ℹ️ Protein structure alignment algorithm based on the TM-score
🍺 brew install brewsci/bio/tmalign
🏡 https://zhanglab.ccmb.med.umich.edu/TM-align/
📖 https://doi.org/10.1093/nar/gki524

[sjackman]

🎉 New formula percolator in Brewsci/bio for Linux and macOS!
ℹ️ Semi-supervised learning for peptide identification from shotgun proteomics data
🍺 brew install brewsci/bio/percolator
🏡 http://percolator.ms
📖 https://doi.org/10.1038/nmeth1113

[sjackman]

🎉 New formula mican in Brewsci/bio for Linux and macOS!
ℹ️ Structure alignment algorithm that can handle Multiple-chain complexes
🍺 brew install brewsci/bio/mican
🏡 http://www.tbp.cse.nagoya-u.ac.jp/MICAN
📖 https://doi.org/10.1186/1471-2105-14-24

[sjackman]

🎉 New formula jmol in Brewsci/bio for Linux and macOS!
ℹ️ Open-source Java viewer for chemical structures in 3D
🍺 brew install brewsci/bio/jmol
🏡 https://jmol.sourceforge.io/

[sjackman]

🎉 New formula plink2 in Brewsci/bio for Linux and macOS!
ℹ️ Analyze genotype and phenotype data
🍺 brew install brewsci/bio/plink2
🏡 https://www.cog-genomics.org/plink2
📖 https://doi.org/10.1186/s13742-015-0047-8

[sjackman]

🎉 New formula slim in Brewsci/bio for Linux and macOS!
ℹ️ Forward simulator for population genetics and evolutionary biology
🍺 brew install brewsci/bio/slim
🏡 https://messerlab.org/slim/
📖 https://doi.org/10.1093/molbev/msy228

[sjackman]

🎉 New formula falco in Brewsci/bio for Linux and macOS!
ℹ️ C++ implementation of FastQC for quality control of sequencing data
🍺 brew install brewsci/bio/falco
🏡 https://github.com/smithlabcode/falco
📖 https://doi.org/10.12688/f1000research.21142.2

[sjackman]

🎉 New formula faqcs in Brewsci/bio for Linux and macOS!
ℹ️ Quality Control of Next Generation Sequencing Data
🍺 brew install brewsci/bio/faqcs
🏡 https://github.com/LANL-Bioinformatics/FaQCs
📖 https://doi.org/10.1186/s12859-014-0366-2

[sjackman]

🎉 New formula raster3d in Brewsci/bio for Linux and macOS!
ℹ️ Set of tools for generating high quality raster images of proteins
🍺 brew install brewsci/bio/raster3d
🏡 http://www.bmsc.washington.edu/raster3d
📖 https://doi.org/10.1016/S0263-7855(98)80030-1

[sjackman]

🎉 New formula mmdb2 in Brewsci/bio for Linux and macOS!
ℹ️ C++ toolkit for working with macromolecular coordinate files
🍺 brew install brewsci/bio/mmdb2
🏡 https://www2.mrc-lmb.cam.ac.uk/

[sjackman]

🎉 New formula libccp4 in Brewsci/bio for Linux and macOS!
ℹ️ Protein X-ray crystallography toolkit
🍺 brew install brewsci/bio/libccp4
🏡 https://www.ccp4.ac.uk/

[sjackman]

🎉 New formula ssm in Brewsci/bio for Linux and macOS!
ℹ️ Secondary-structure matching, tool for fast protein structure alignment
🍺 brew install brewsci/bio/ssm
🏡 https://www2.mrc-lmb.cam.ac.uk
📖 https://doi.org/10.1107/S0907444904026460

[sjackman]

🎉 New formula clipper4coot in Brewsci/bio for Linux and macOS!
ℹ️ Crystallographic automation and complex data manipulation libraries
🍺 brew install brewsci/bio/clipper4coot
🏡 https://www2.mrc-lmb.cam.ac.uk/

[sjackman]

🎉 New formula krona in Brewsci/bio for Linux and macOS!
ℹ️ Interactively explore metagenomes and more from a web browser
🍺 brew install brewsci/bio/krona
🏡 https://github.com/marbl/Krona/wiki
📖 https://doi.org/10.1186/1471-2105-12-385

[sjackman]

🎉 New formula biointerchange in Brewsci/bio for Linux and macOS!
ℹ️ Genomic linked-data converter: an interchange GFF, GVF, VCF files via JSON-LD
🍺 brew install brewsci/bio/biointerchange
🏡 https://github.com/BioInterchange/BioInterchangeC