Updates

[sjackman]

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[sjackman]

🎉 New formula mpboot in Brewsci/bio for Linux and macOS! ℹ️ Fast maximum parsimony tree inference and bootstrap approximation 🍺 brew install brewsci/bio/mpboot 🏡 http://www.iqtree.org/mpboot/ 📖 https://doi.org/10.1186/s12862-018-1131-3

[jonchang]

🎉 New formula phyx in Brewsci/bio for Linux and macOS! ℹ️ Command-line tools for phylogenetic analyses 🍺 brew install brewsci/bio/phyx 🏡 https://github.com/FePhyFoFum/phyx 📖 https://doi.org/10.1093/bioinformatics/btx063

[sjackman]

🎉 New formula bcalm in Brewsci/bio for Linux and macOS! ℹ️ De Bruijn graph compaction in low memory 🍺 brew install brewsci/bio/bcalm 🏡 https://github.com/GATB/bcalm 📖 https://doi.org/10.1093/bioinformatics/btw279

[tseemann]

🎉 New formula orfm in Brewsci/bio for Linux and macOS! ℹ️ Simple and not slow ORF caller for NGS reads 🍺 brew install brewsci/bio/orfm 🏡 https://github.com/wwood/OrfM 📖 https://doi.org/10.1093/bioinformatics/btw241

[sjackman]

🎉 New formula links-scaffolder in Brewsci/bio for Linux and macOS! ℹ️ Long Interval Nucleotide K-mer Scaffolder 🍺 brew install brewsci/bio/links-scaffolder 🏡 http://www.bcgsc.ca/platform/bioinfo/software/links 📖 https://doi.org/10.1186/s13742-015-0076-3

[tseemann]

🎉 New formula kma in Brewsci/bio for Linux and macOS! ℹ️ Align long and short reads to redundant sequence databases 🍺 brew install brewsci/bio/kma 🏡 https://bitbucket.org/genomicepidemiology/kma

[tseemann]

🎉 New formula genome-painter in Brewsci/bio for Linux and macOS! ℹ️ Paint genomes with taxa-specific k-mer probabilities 🍺 brew install brewsci/bio/genome-painter 🏡 https://github.com/scwatts/genome_painter

[jonchang]

🎉 New formula seq-gen in Brewsci/bio for Linux and macOS! ℹ️ Simulator of DNA and amino acid sequence evolution 🍺 brew install brewsci/bio/seq-gen 🏡 http://tree.bio.ed.ac.uk/software/seqgen/ 📖 https://doi.org/10.1093/bioinformatics/13.3.235

[jonchang]

🎉 New formula bali-phy in Brewsci/bio for Linux and macOS! ℹ️ Bayesian co-estimation of phylogenies and multiple alignments 🍺 brew install brewsci/bio/bali-phy 🏡 http://www.bali-phy.org/ 📖 http://dx.doi.org/10.1093/bioinformatics/btl175

[jonchang]

🎉 New formula biomake in Brewsci/bio for Linux and macOS! ℹ️ GNU-Make-like utility for managing builds and complex workflows 🍺 brew install brewsci/bio/biomake 🏡 https://github.com/evoldoers/biomake 📖 https://doi.org/10.1101/093245

[sjackman]

🎉 New formula pymol in Brewsci/bio for Linux and macOS! ℹ️ molecular visualization system 🍺 brew install brewsci/bio/pymol 🏡 https://pymol.org/

[sjackman]

🎉 New formula circlator in Brewsci/bio for Linux and macOS! ℹ️ Tool to circularize genome assemblies 🍺 brew install brewsci/bio/circlator 🏡 https://sanger-pathogens.github.io/circlator/ 📖 https://doi.org/10.1186/s13059-015-0849-0

[sjackman]

🎉 New formula breseq in Brewsci/bio for Linux and macOS! ℹ️ Find mutations in microbes from short reads 🍺 brew install brewsci/bio/breseq 🏡 http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing

[sjackman]

🎉 New formula edirect in Brewsci/bio for Linux and macOS! ℹ️ Access NCBI databases via the command-line 🍺 brew install brewsci/bio/edirect 🏡 https://www.ncbi.nlm.nih.gov/books/NBK179288/

[sjackman]

🎉 New formula smalt in Brewsci/bio for Linux and macOS! ℹ️ Aligns DNA sequencing reads with a reference genome 🍺 brew install brewsci/bio/smalt 🏡 https://www.sanger.ac.uk/science/tools/smalt-0

[sjackman]

🎉 New formula lrsim in Brewsci/bio for Linux and macOS! ℹ️ 10x Genomics Reads Simulator 🍺 brew install brewsci/bio/lrsim 🏡 https://github.com/aquaskyline/LRSIM

[sjackman]

🎉 New formula iva in Brewsci/bio for Linux and macOS! ℹ️ Iterative Virus Assembler 🍺 brew install brewsci/bio/iva 🏡 https://github.com/sanger-pathogens/iva 📖 https://doi.org/10.1093/bioinformatics/btv120

[sjackman]

🎉 New formula cutadapt in Brewsci/bio for Linux and macOS! ℹ️ Removes adapter sequences, primers, and poly-A tails 🍺 brew install brewsci/bio/cutadapt 🏡 https://github.com/marcelm/cutadapt 📖 https://doi.org/10.14806/ej.17.1.200

[sjackman]

🎉 New formula ale in Brewsci/bio for Linux and macOS! ℹ️ Assembly Likelihood Estimator 🍺 brew install brewsci/bio/ale 🏡 https://github.com/sc932/ALE 📖 https://doi.org/10.1093/bioinformatics/bts723

[tseemann]

🎉 New formula sumaclust in Brewsci/bio for Linux and macOS! ℹ️ Fast and exact sequence clustering for DNA metabarcoding 🍺 brew install brewsci/bio/sumaclust 🏡 https://git.metabarcoding.org/obitools/sumaclust/wikis/home

[sjackman]

🎉 New formula express in Brewsci/bio for Linux and macOS! ℹ️ Streaming quantification for sequencing 🍺 brew install brewsci/bio/express 🏡 http://bio.math.berkeley.edu/eXpress/ 📖 https://doi.org/10.1038/nmeth.2251

[sjackman]

🎉 New formula jellyfish in Brewsci/bio for Linux and macOS! ℹ️ Fast, memory-efficient counting of DNA k-mers 🍺 brew install brewsci/bio/jellyfish 🏡 http://www.genome.umd.edu/jellyfish.html 📖 https://doi.org/10.1093/bioinformatics/btr011

[sjackman]

🎉 New formula trinity in Brewsci/bio for Linux and macOS! ℹ️ RNA-Seq de novo assembler 🍺 brew install brewsci/bio/trinity 🏡 https://trinityrnaseq.github.io 📖 https://doi.org/10.1038/nbt.1883

[sjackman]

🎉 New formula maxbin2 in Brewsci/bio for Linux and macOS! ℹ️ Binning algorithm to recover genomes from metagenomic datasets 🍺 brew install brewsci/bio/maxbin2 🏡 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html 📖 https://doi.org/10.1093/bioinformatics/btv638

[tseemann]

🎉 New formula salmid in Brewsci/bio for Linux and macOS! ℹ️ Rapid confirmation of Salmonella species from WGS 🍺 brew install brewsci/bio/salmid 🏡 https://github.com/hcdenbakker/SalmID

[tseemann]

🎉 New formula indel-seq-gen in Brewsci/bio for Linux! ℹ️ Sequence simulation for divergent DNA and AA families 🍺 brew install brewsci/bio/indel-seq-gen 🏡 http://bioinfolab.unl.edu/~cstrope/iSG/ 📖 https://doi.org/10.1093/molbev/msp174

[tseemann]

🎉 New formula parsnp in Brewsci/bio for Linux and macOS! ℹ️ Microbial core genome alignment and SNP detection 🍺 brew install brewsci/bio/parsnp 🏡 https://github.com/marbl/parsnp 📖 https://doi.org/10.1186/s13059-014-0524-x

[sjackman]

🎉 New formula quip in Brewsci/bio for Linux and macOS! ℹ️ Compressing NGS data with extreme prejudice 🍺 brew install brewsci/bio/quip 🏡 https://homes.cs.washington.edu/~dcjones/quip 📖 https://doi.org/10.1093/nar/gks754

[sjackman]

🎉 New formula indelible in Brewsci/bio for Linux and macOS! ℹ️ Flexible Simulator of Biological Sequence Evolution 🍺 brew install brewsci/bio/indelible 🏡 http://abacus.gene.ucl.ac.uk/software/indelible/ 📖 https://doi.org/10.1093/molbev/msp098

[jonchang]

🎉 New formula rcorrector in Brewsci/bio for Linux and macOS! ℹ️ Error correction for Illumina RNA-seq reads 🍺 brew install brewsci/bio/rcorrector 🏡 https://github.com/mourisl/Rcorrector 📖 https://doi.org/10.1186/s13742-015-0089-y

[sjackman]

🎉 New formula flowcraft in Brewsci/bio for Linux and macOS! ℹ️ Nextflow pipeline assembler for genomics 🍺 brew install brewsci/bio/flowcraft 🏡 https://github.com/assemblerflow/flowcraft

[sjackman]

🎉 New formula trimadap in Brewsci/bio for Linux and macOS! ℹ️ Fast but inaccurate adapter trimmer for Illumina reads 🍺 brew install brewsci/bio/trimadap 🏡 https://github.com/lh3/trimadap

[tseemann]

🎉 New formula filtlong in Brewsci/bio for Linux and macOS! ℹ️ Quality filtering of long noisy DNA sequencing reads by @rrwick 🍺 brew install brewsci/bio/filtlong 🏡 https://github.com/rrwick/Filtlong

[tseemann]

🎉 New formula ngmaster in Brewsci/bio for Linux and macOS! ℹ️ NG-MAST genotyping for Neisseria gonorrhoeae by @kwongj 🍺 brew install brewsci/bio/ngmaster 🏡 https://github.com/MDU-PHL/ngmaster

[tseemann]

🎉 New formula bfc in Brewsci/bio for Linux and macOS! ℹ️ High-performance error correction for Illumina resequencing data 🍺 brew install brewsci/bio/bfc 🏡 https://github.com/lh3/bfc

[sjackman]

🎉 New formula nxrepair in Brewsci/bio for macOS! ℹ️ Correct errors in genome sequence assemblies using mate pair reads 🍺 brew install brewsci/bio/nxrepair 🏡 https://github.com/rebeccaroisin/nxrepair 📖 https://doi.org/10.7717/peerj.996

[tseemann]

🎉 New formula taxonkit in Brewsci/bio for Linux and macOS! ℹ️ Cross-platform and efficient NCBI taxonomy toolkit 🍺 brew install brewsci/bio/taxonkit 🏡 https://github.com/shenwei356/taxonkit 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[sjackman]

🎉 New formula gfaview in Brewsci/bio for Linux and macOS! ℹ️ Manipulate an assembly graph in GFA format 🍺 brew install brewsci/bio/gfaview 🏡 https://github.com/lh3/gfa1

[tseemann]

🎉 New formula bazam in Brewsci/bio for Linux and macOS! ℹ️ Extract paired reads from coordinate sorted BAM files 🍺 brew install brewsci/bio/bazam 🏡 https://github.com/ssadedin/bazam 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[tseemann]

🎉 New formula swipe in Brewsci/bio for Linux and macOS! ℹ️ Smith-Waterman database searches with inter-sequence SIMD parallelisation 🍺 brew install brewsci/bio/swipe 🏡 http://dna.uio.no/swipe/ 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[tseemann]

🎉 New formula skesa in Brewsci/bio for Linux and macOS! ℹ️ Strategic Kmer Extension for Scrupulous Assemblies 🍺 brew install brewsci/bio/skesa 🏡 https://github.com/ncbi/SKESA 📖 https://doi.org/10.1186/s13059-018-1540-z 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[sjackman]

🎉 New formula transabyss in Brewsci/bio for Linux! ℹ️ De novo assembly of RNA-seq data using ABySS 🍺 brew install brewsci/bio/transabyss 🏡 https://github.com/bcgsc/transabyss 📖 https://doi.org/10.1038/nmeth.1517

[tseemann]

🎉 New formula parasail in Brewsci/bio for Linux! ℹ️ Pairwise Sequence Alignment Library 🍺 brew install brewsci/bio/parasail 🏡 https://github.com/jeffdaily/parasail 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[sjackman]

🎉 New formula sambamba in Brewsci/bio for Linux and macOS! ℹ️ Tools for working with SAM/BAM data 🍺 brew install brewsci/bio/sambamba 🏡 https://lomereiter.github.io/sambamba 📖 https://doi.org/10.1093/bioinformatics/btv098

[sjackman]

🎉 New formula kmergenie in Brewsci/bio for Linux and macOS! ℹ️ Estimates the best k-mer length for genome de novo assembly 🍺 brew install brewsci/bio/kmergenie 🏡 http://kmergenie.bx.psu.edu/ 📖 https://doi.org/10.1093/bioinformatics/btt310

[tseemann]

🎉 New formula kaiju in Brewsci/science for Linux and macOS! ℹ️ Fast taxonomic classification of metagenomic sequencing reads 🍺 brew install brewsci/science/kaiju 🏡 http://kaiju.binf.ku.dk/ 🔬 https://github.com/brewsci/homebrew-science 🐧 http://linuxbrew.sh #bioinformatics

[tseemann]

🎉 New formula unikmer in Brewsci/bio for Linux and macOS! ℹ️ Manipulate small kmers without frequency information 🍺 brew install brewsci/bio/unikmer 🏡 https://github.com/shenwei356/unikmer 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[tseemann]

🎉 New formula wtdbg2 in Brewsci/bio for Linux! ℹ️ Fuzzy de Bruijn Graph long read assembler 🍺 brew install brewsci/bio/wtdbg2 🏡 https://github.com/ruanjue/wtdbg2 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics

[tseemann]

🎉 New formula ska in Brewsci/bio for Linux and macOS! ℹ️ Split Kmer Analysis toolkit 🍺 brew install brewsci/bio/ska 🏡 https://github.com/simonrharris/SKA/releases 🔬 https://github.com/brewsci/homebrew-bio 🐧 http://linuxbrew.sh #bioinformatics @simonrharris

[sjackman]

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