traits-finder 1.0

# traits_finder ## Introduction * traits_finder searches and summarizes traits in genomes and metagenomes * input: reference database and folder of genomes/metagenomes * requirement: blast or hmm * requirement: for hmm, you need to prepare the hmm database * optional: diamond, bwa, hs-blastn, usearch

## Install pip install traits_finderin preparation: anaconda download caozhichongchong/traits_finder

## Availability

https://pypi.org/project/traits_finder

## How to use it 1. search protein reference sequences in genomes by similarity searchtraits_finder -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 -inf 1 -s 1

2. search protein reference sequences in metagenomes by similarity searchtraits_finder -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 -inf 2 -s 1

3. search dna reference sequences in genomes by similarity searchtraits_finder -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 -inf 1 -s 1

4. search dba reference sequences in metagenomes by similarity searchtraits_finder -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 -inf 2 -s 1

5. search protein reference sequences in genomes by hmmtraits_finder -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 -inf 1 -s 2

6. search dna reference sequences in genomes by alignmenttraits_finder -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 -inf 1 -s 1

7. search dna reference sequences in metagenomes by alignmenttraits_finder -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 -inf 2 -s 1

## Results

## Copyright Copyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MITCitation: Not yet, coming soon!Contact: anniz44@mit.edu