Package: traits-finder
traits_finderIntroductiontraits_finder searches and summarizes traits in genomes and metagenomesinput: reference database and folder of genomes/metagenomesrequirement: python >= 3.0, blast or hmmrequirement: for hmm, you need to prepare the hmm databaseoptional: diamond, bwa, hs-blastn, usearch, mafft, fasttreeInstallpip install traits_finderin preparation:anaconda download caozhichongchong/traits_finderlatest version (unstable though)git clone https://github.com/caozhichongchong/traits_finder.gitcd traits_finderpython setup.py buildpython setup.py installAvailabilityhttps://pypi.org/project/traits_finderWhat do you need to prepareyour reference database (-db your.db), protein sequences (-dbf 1) or dna sequences (-dbf 2)a mapping file of functions to each reference sequence (sequence	function)all genomes/metagenomes in a folder (-i your.input.folder)suffix or file extension of your genomes/metagenomes, such as .fasta or .fastq (-fa your.input.genome/metagenome.format)programs to run: blast for similarity search (-s 1 )or hmm for domain search (-s 2)optional programs to speedup! diamond, hs-blastn (or usearch for 16S extracting), usearch (necessary for HGT and HGT_sum)optional programs to look at sequence variants! bwa, mafft, fasttreeHow to use itSearch traits: boring and slow...Database installed in traits_finder: antibiotic resistant genes (-db ARG), butyrate producing genes (-db but)search protein reference sequences in genomes (traits_finder genome) or mobile genetic elements (traits_finder mge) by similarity searchtraits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1\search protein reference sequences in metagenomes by similarity searchtraits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1\search dna reference sequences in genomes by similarity searchtraits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1\search dba reference sequences in metagenomes by similarity searchtraits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1\search protein reference sequences in genomes by hmmtraits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --hmm hmmscan -dbf 1 -s 2\search dna reference sequences in genomes by alignmenttraits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1\search dna reference sequences in metagenomes by alignmenttraits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1\Summarize results: cool and fast!summarize traits in genometraits_finder sum_genome -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s\summarize traits in metagenomestraits_finder sum_meta -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --meta metadata.txt\HGT finder and summarizing: cool and fast! (still-testing)ResultsCopyrightCopyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MITCitation: Not yet, coming soon!Contact:anniz44@mit.edu