Updates

[sjackman]

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

[tseemann]

🎉 New formula dwgsim in Brewsci/bio for Linux and macOS! ℹ️ Whole Genome Simulator for Next-Generation Sequencing 🍺 brew install brewsci/bio/dwgsim 🏡 https://github.com/nh13/DWGSIM

[tseemann]

🎉 New formula last in Brewsci/bio for Linux and macOS! ℹ️ Find similar regions between sequences 🍺 brew install brewsci/bio/last 🏡 http://last.cbrc.jp/ 📖 https://doi.org/10.1101/gr.113985.110

[tseemann]

🎉 New formula lastz in Brewsci/bio for Linux and macOS! ℹ️ Align DNA sequences, a pairwise aligner 🍺 brew install brewsci/bio/lastz 🏡 https://www.bx.psu.edu/~rsharris/lastz/

[tseemann]

🎉 New formula rtg-tools in Brewsci/bio for Linux and macOS! ℹ️ Easily manipulate and accurately compare multiple VCF files 🍺 brew install brewsci/bio/rtg-tools 🏡 https://www.realtimegenomics.com/products/rtg-tools 📖 https://doi.org/10.1101/023754

[jonchang]

🎉 New formula exabayes in Brewsci/bio for Linux and macOS! ℹ️ Large-scale Bayesian tree inference 🍺 brew install brewsci/bio/exabayes 🏡 https://sco.h-its.org/exelixis/web/software/exabayes/ 📖 https://doi.org/10.1093/molbev/msu236

[jonchang]

🎉 New formula r8s in Brewsci/bio for Linux and macOS! ℹ️ Estimate rates and divergence times on phylogenetic trees 🍺 brew install brewsci/bio/r8s 🏡 https://ceiba.biosci.arizona.edu/r8s/ 📖 https://doi.org/10.1093/bioinformatics/19.2.301

[tseemann]

🎉 New formula berokka in Brewsci/bio for Linux and macOS! ℹ️ Trim, circularise, and orient long read assemblies 🍺 brew install brewsci/bio/berokka 🏡 https://github.com/tseemann/berokka

[tseemann]

🎉 New formula snpeff in Brewsci/bio for Linux and macOS! ℹ️ Genetic variant annotation and effect prediction toolbox 🍺 brew install brewsci/bio/snpeff 🏡 https://snpeff.sourceforge.io/ 📖 https://doi.org/10.4161/fly.19695

[sjackman]

🎉 New formula biobloomtools in Brewsci/bio for Linux and macOS! ℹ️ BioBloom Tools (BBT): Bloom filter for bioinformatics 🍺 brew install brewsci/bio/biobloomtools 🏡 http://www.bcgsc.ca/platform/bioinfo/software/biobloomtools/ 📖 https://doi.org/10.1093/bioinformatics/btu558

[sjackman]

🎉 New formula dida in Brewsci/bio for Linux and macOS! ℹ️ Distributed Indexing Dispatched Alignment 🍺 brew install brewsci/bio/dida 🏡 http://www.bcgsc.ca/platform/bioinfo/software/dida 📖 https://doi.org/10.1371/journal.pone.0126409

[jonchang]

🎉 New formula libpll in Brewsci/bio for Linux and macOS! ℹ️ Phylogenetic likelihood library 🍺 brew install brewsci/bio/libpll 🏡 http://www.libpll.org/ 📖 https://doi.org/10.1093/sysbio/syu084

[jonchang]

🎉 New formula astral in Brewsci/bio for Linux and macOS! ℹ️ Estimate species tree given set of unrooted gene trees 🍺 brew install brewsci/bio/astral 🏡 https://github.com/smirarab/ASTRAL 📖 https://doi.org/10.1007/978-3-319-67979-2_4

[jonchang]

🎉 New formula bamm in Brewsci/bio for Linux and macOS! ℹ️ Bayesian analysis of macroevolutionary mixture models on phylogenies 🍺 brew install brewsci/bio/bamm 🏡 http://bamm-project.org 📖 https://doi.org/10.1371/journal.pone.0089543

[sjackman]

🎉 New formula nxtrim in Brewsci/bio for Linux and macOS! ℹ️ Trim adapters for Illumina Nextera Mate Pair libraries 🍺 brew install brewsci/bio/nxtrim 🏡 https://github.com/sequencing/NxTrim 📖 https://doi.org/10.1101/007666

[sjackman]

🎉 New formula ema in Brewsci/bio for Linux and macOS! ℹ️ Fast and accurate alignment of linked reads 🍺 brew install brewsci/bio/ema 🏡 http://ema.csail.mit.edu 📖 https://doi.org/10.1101/220236

[tseemann]

🎉 New formula raxml-ng in Brewsci/bio for Linux and macOS! ℹ️ RAxML Next Generation: faster, easier-to-use and more flexible 🍺 brew install brewsci/bio/raxml-ng 🏡 https://sco.h-its.org/exelixis/web/software/raxml/ (via @jonchang)

[tseemann]

🎉 New formula vcflib in Brewsci/bio for Linux and macOS! ℹ️ Command-line tools for manipulating VCF files 🍺 brew install brewsci/bio/vcflib 🏡 https://github.com/ekg/vcflib

[tseemann]

🎉 New formula freebayes in Brewsci/bio for Linux and macOS! ℹ️ Bayesian variant discovery and genotyping 🍺 brew install brewsci/bio/freebayes 🏡 https://github.com/ekg/freebayes 📖 https://arxiv.org/abs/1207.3907v2

[tseemann]

🎉 New formula clonalframeml in Brewsci/bio for Linux and macOS! ℹ️ Efficient Inference of Recombination in Bacterial Genomes 🍺 brew install brewsci/bio/clonalframeml 🏡 https://github.com/xavierdidelot/ClonalFrameML 📖 https://doi.org/10.1371/journal.pcbi.1004041

[sjackman]

🎉 New formula fasttree in Brewsci/bio for Linux and macOS! ℹ️ Approximately-maximum-likelihood phylogenetic trees 🍺 brew install brewsci/bio/fasttree 🏡 http://microbesonline.org/fasttree/ 📖 https://doi.org/10.1371/journal.pone.0009490

[sjackman]

🎉 New formula snp-sites in Brewsci/bio for Linux and macOS! ℹ️ Find SNP sites in a multi FASTA alignment file 🍺 brew install brewsci/bio/snp-sites 🏡 https://github.com/sanger-pathogens/snp-sites 📖 https://doi.org/10.1099/mgen.0.000056

[sjackman]

🎉 New formula megahit in Brewsci/bio for Linux and macOS! ℹ️ Ultra-fast SMP/GPU succinct DBG metagenome assembly 🍺 brew install brewsci/bio/megahit 🏡 https://github.com/voutcn/megahit 📖 https://doi.org/10.1093/bioinformatics/btv033

[sjackman]

🎉 New formula bonsai in Brewsci/bio for Linux and macOS! ℹ️ Ultrafast, flexible taxonomic analysis and classification 🍺 brew install brewsci/bio/bonsai 🏡 https://github.com/dnbaker/bonsai

[sjackman]

🎉 New formula mafft in Homebrew/core for Linux and macOS! ℹ️ Multiple alignments with fast Fourier transforms 🍺 brew install mafft 🏡 https://mafft.cbrc.jp/alignment/software/

[tseemann]

🎉 New formula prank in Brewsci/bio for Linux and macOS! ℹ️ Multiple alignment for DNA, codon and amino-acid sequences 🍺 brew install brewsci/bio/prank 🏡 http://wasabiapp.org/software/prank/

[tseemann]

🎉 New formula bonsai in Brewsci/bio for Linux and macOS! ℹ️ Ultrafast, flexible taxonomic analysis and classification 🍺 brew install brewsci/bio/bonsai 🏡 https://github.com/dnbaker/bonsai

[tseemann]

🎉 New formula elph in Brewsci/bio for Linux and macOS! ℹ️ Gibbs sampler for finding motifs in DNA or protein sequences 🍺 brew install brewsci/bio/elph 🏡 http://www.cbcb.umd.edu/software/elph/

[sjackman]

🎉 New formula hisat2 in Brewsci/bio for Linux and macOS! ℹ️ Graph-based alignment to a population of genomes 🍺 brew install brewsci/bio/hisat2 🏡 https://ccb.jhu.edu/software/hisat2/ 📖 https://doi.org/10.1038/nmeth.3317

[jonchang]

🎉 New formula beast2 in Brewsci/bio for Linux and macOS! ℹ️ Bayesian evolutionary analysis by sampling trees 🍺 brew install brewsci/bio/beast2 🏡 https://www.beast2.org/ 📖 https://doi.org/10.1371/journal.pcbi.1003537

[tseemann]

🎉 New formula fastuniq in Brewsci/bio for Linux and macOS! ℹ️ Fast de novo duplicate removal for paired short reads 🍺 brew install brewsci/bio/fastuniq 🏡 https://sourceforge.net/projects/fastuniq/ 📖 https://doi.org/10.1371/journal.pone.0052249

[jonchang]

🎉 New formula beagle in Brewsci/bio for Linux and macOS! ℹ️ Evaluate the likelihood of sequence evolution on trees 🍺 brew install brewsci/bio/beagle 🏡 https://github.com/beagle-dev/beagle-lib 📖 https://doi.org/10.1093/sysbio/syr100

[jonchang]

🎉 New formula mrbayes in Brewsci/bio for Linux and macOS! ℹ️ Bayesian inference of phylogenies and evolutionary models 🍺 brew install brewsci/bio/mrbayes 🏡 https://mrbayes.sourceforge.io/ 📖 https://doi.org/10.1093/bioinformatics/btg180

[tseemann]

🎉 New formula cd-hit in Brewsci/bio for Linux and macOS! ℹ️ Cluster and compare protein or nucleotide sequences 🍺 brew install brewsci/bio/cd-hit 🏡 http://cd-hit.org 📖 https://doi.org/10.1093/bioinformatics/btl158

[tseemann]

🎉 New formula andi in Brewsci/bio for Linux and macOS! ℹ️ Estimate evolutionary distance between similar genomes 🍺 brew install brewsci/bio/andi 🏡 https://github.com/EvolBioInf/andi 📖 https://doi.org/10.1093/bioinformatics/btu815

[tseemann]

🎉 New formula centrifuge in Brewsci/bio for Linux! ℹ️ Rapid sensitive classification of metagenomic sequences 🍺 brew install brewsci/bio/centrifuge 🏡 http://www.ccb.jhu.edu/software/centrifuge 📖 https://doi.org/10.1101/gr.210641.116

[tseemann]

🎉 New formula idba in Brewsci/bio for Linux and macOS! ℹ️ Iterative De Bruijn Graph De Novo Assembler for sequence assembly 🍺 brew install brewsci/bio/idba 🏡 https://i.cs.hku.hk/~alse/hkubrg/projects/idba/ 📖 https://doi.org/10.1093/bioinformatics/bts174

[tseemann]

🎉 New formula finch-rs in Brewsci/bio for Linux and macOS! ℹ️ Genomic minhashing implementation in Rust 🍺 brew install brewsci/bio/finch-rs 🏡 https://github.com/onecodex/finch-rs

[tseemann]

🎉 New formula k8 in Brewsci/bio for Linux and macOS! ℹ️ Javascript shell based on Google's V8 Javascript engine 🍺 brew install brewsci/bio/k8 🏡 https://github.com/attractivechaos/k8

[tseemann]

🎉 New formula fasta in Brewsci/bio for Linux and macOS! ℹ️ Classic FASTA sequence alignment suite 🍺 brew install brewsci/bio/fasta 🏡 http://faculty.virginia.edu/wrpearson/fasta/ 📖 https://doi.org/10.1016/0076-6879(90)83007-V

[sjackman]

🎉 New formula tigmint in Brewsci/bio for Linux and macOS! ℹ️ Correct misassemblies using linked reads 🍺 brew install brewsci/bio/tigmint 🏡 https://bcgsc.github.io/tigmint/ 📖 https://doi.org/10.1101/304253

[sjackman]

🎉 New formula fermi-lite in Brewsci/bio for Linux and macOS! ℹ️ Assembling Illumina short reads in small regions 🍺 brew install brewsci/bio/fermi-lite 🏡 https://github.com/lh3/fermi-lite 📖 https://doi.org/10.1093/bioinformatics/bts280

[sjackman]

🎉 New formula flye in Brewsci/bio for Linux and macOS! ℹ️ Fast and accurate de novo assembler for single molecule sequencing reads 🍺 brew install brewsci/bio/flye 🏡 https://github.com/fenderglass/Flye 📖 https://doi.org/10.1101/247148

[tseemann]

🎉 New formula realphy in Brewsci/bio for Linux and macOS! ℹ️ The Reference sequence Alignment based Phylogeny 🍺 brew install brewsci/bio/realphy 🏡 https://realphy.unibas.ch/fcgi/realphy 📖 https://doi.org/10.1093/molbev/msu088

[sjackman]

🎉 New formula gfalint in Brewsci/bio for Linux and macOS! ℹ️ Check a GFA file for syntax errors 🍺 brew install brewsci/bio/gfalint 🏡 http://sjackman.ca/gfalint/

[sjackman]

🎉 New formula blat in Brewsci/bio for Linux and macOS! ℹ️ Genomic sequence search tool 🍺 brew install brewsci/bio/blat 🏡 https://genome.ucsc.edu/FAQ/FAQblat.html 📖 https://doi.org/10.1101/gr.229202

[sjackman]

🎉 New formula gmap-gsnap in Brewsci/bio for Linux and macOS! ℹ️ Genomic Mapping & Alignment Program for RNA/EST/Short-read sequences 🍺 brew install brewsci/bio/gmap-gsnap 🏡 http://research-pub.gene.com/gmap/ 📖 https://doi.org/10.1093/bioinformatics/btq057

[sjackman]

🎉 New formula humann2 in Brewsci/bio for Linux and macOS! ℹ️ HUMAnN2: The HMP Unified Metabolic Analysis Network 🍺 brew install brewsci/bio/humann2 🏡 https://huttenhower.sph.harvard.edu/humann 📖 https://doi.org/10.1371/journal.pcbi.1002358

[tseemann]

🎉 New formula samclip in Brewsci/bio for Linux and macOS! ℹ️ Filter soft/hard clipped alignments from SAM files 🍺 brew install brewsci/bio/samclip 🏡 https://github.com/tseemann/samclip

[sjackman]

🎉 New formula phlawd in Brewsci/bio for Linux and macOS! ℹ️ Phylogenetic dataset construction 🍺 brew install brewsci/bio/phlawd 🏡 https://github.com/jonchang/phlawd 📖 https://doi.org/10.1186/1471-2148-9-37

[sjackman]

🎉 New formula quickmerge in Brewsci/bio for Linux and macOS! ℹ️ Merge long read and short read assemblies 🍺 brew install brewsci/bio/quickmerge 🏡 https://github.com/mahulchak/quickmerge 📖 https://doi.org/10.1093/nar/gkw654