From 908561e8760d3c71270125adb2187622182c3cf6 Mon Sep 17 00:00:00 2001
From: Haikel Bogale <70728342+Haikelnb@users.noreply.github.com>
Date: Tue, 24 Oct 2023 13:59:52 -0400
Subject: [PATCH] Create README.md

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+# blast+ container
+
+Main tools:
+
+- [blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+
+This is meant to assist in local blast searches. No blast databases will be maintained in this container. Be sure to mount your relevant Volumes with `--volumes` or `-v` when using the command line.
+
+blast+ is actually a suite of tools. blast+ v.2.14.1 includes:
+
+```bash
+$ ls /ncbi-blast-2.14.1+/bin
+blast_formatter
+blast_formatter_vdb
+blast_vdb_cmd
+blastdb_aliastool
+blastdbcheck
+blastdbcmd
+blastn
+blastn_vdb
+blastp
+blastx
+cleanup-blastdb-volumes.py
+convert2blastmask
+deltablast
+dustmasker
+get_species_taxids.sh
+legacy_blast.pl
+makeblastdb
+makembindex
+makeprofiledb
+psiblast
+rpsblast
+rpstblastn
+segmasker
+tblastn
+tblastn_vdb
+tblastx
+update_blastdb.pl
+windowmasker 
+```
+
+Currently not supported, but could be:
+
+```bash
+get_species_taxids.sh # requires E-direct
+update_blastdb.pl     # requires perl
+```
+
+## Example Usage
+
+```bash
+# making a blast database
+makeblastdb -dbtype nucl -in fasta.fa
+
+# query
+tblastn -query query.fasta -db fasta.fa -outfmt '6' -out blast_hits.txt
+```
+
+More documentation can be found at [https://www.ncbi.nlm.nih.gov/books/NBK569856/](https://www.ncbi.nlm.nih.gov/books/NBK569856/) and [https://www.ncbi.nlm.nih.gov/books/NBK279690/](https://www.ncbi.nlm.nih.gov/books/NBK279690/)