diff --git a/README.md b/README.md index 16f0372..009e15f 100644 --- a/README.md +++ b/README.md @@ -3,28 +3,29 @@ This program is made to help you mining NCBI BLAST output. -### Requirements +## Requirements Before able to execute `blastMining`, you need to install the following programs and make sure that they are executable and available in your `PATH`: -* __ [NCBI BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) __ +* [NCBI BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) -* __ [TaxonKit - NCBI Taxonomy Toolkit](https://bioinf.shenwei.me/taxonkit/) __: -`Please install` this program and download `taxdump`. Follow their [instruction](https://bioinf.shenwei.me/taxonkit/usage/#before-use) +* [TaxonKit - NCBI Taxonomy Toolkit](https://bioinf.shenwei.me/taxonkit/): + `Please install` this program and download `taxdump`. + Follow their [instruction](https://bioinf.shenwei.me/taxonkit/usage/#before-use) -* __ [csvtk](https://github.com/shenwei356/csvtk) +* [csvtk](https://github.com/shenwei356/csvtk) -* __ Python3 +* [Python3](https://www.python.org/) -### Installation -##### Option 1 +## Installation +### Option 1 You can easily install this package using PyPI ```bash $ pip install blastMining ``` -##### Option 2 +### Option 2 Download the latest realese of blastMining in my Github repository. Then install it using pip @@ -33,7 +34,7 @@ Then install it using pip $ pip install blastMining-0.1.0.tar.gz ``` -### Tutorial +## Tutorial Running blastn ```bash blastn -query test_data/ASV.fasta -db nt -out test_data/BLASTn.out -outfmt="6 qseqid sseqid pident length mismatch gapopen evalue bitscore staxid" -max_target_seqs 10 @@ -42,25 +43,25 @@ blastn -query test_data/ASV.fasta -db nt -out test_data/BLASTn.out -outfmt="6 qs Next, `mining` your blast result with one of the following methods: -##### Method 1. Vote with p. identity cut-off +### Method 1. Vote with p. identity cut-off ```bash $ blastMining vote -i test_data/BLASTn.out -e 1e-03 -n 10 -txl 99,97,95,90,85,80,75 -o Vote_method ``` -##### Method 2. vote to species level for all +### Method 2. vote to species level for all ```bash $ blastMining voteSpecies -i test_data/BLASTn.out -e 1e-03 -n 10 -o VoteSpecies_method ``` -##### Method 3. LCA +### Method 3. LCA ```bash $ blastMining lca -i test_data/BLASTn.out -e 1e-03 -n 10 -o lca_method ``` -##### Command options +## Command options ```bash $ blastMining --help @@ -83,7 +84,7 @@ options: --debug debug mode output [False] ``` -###### Method 1 +### Method 1 ```bash $ blastMining vote --help @@ -108,7 +109,7 @@ options: ``` -###### Method 2 +### Method 2 ```bash $ blastMining voteSpecies --help @@ -128,7 +129,7 @@ options: output ``` -###### Method 3 +### Method 3 ```bash $ blastMining lca --help @@ -149,4 +150,4 @@ options: ``` # Citation -**If you find this package useful, `please cite` (https://github.com/NuruddinKhoiry/blastMining) \ No newline at end of file +**If you find this package useful**, `please cite` (https://github.com/NuruddinKhoiry/blastMining) \ No newline at end of file