From 4fc389e274076f8008a196c9e48df6ab856a5e25 Mon Sep 17 00:00:00 2001
From: mansikath <132908109+mansikath@users.noreply.github.com>
Date: Sun, 26 Nov 2023 13:59:35 +0530
Subject: [PATCH] Update README.md

---
 README.md | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index a9c9e94..4f0a7fa 100644
--- a/README.md
+++ b/README.md
@@ -20,12 +20,15 @@ fastqc SRR26624132_1.fastq SRR26624132_2.fastq
 ```
 ### Step 3: Trimming
 Use Trimmomatic to trim low-quality bases:
+- [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic)
+
 ```bash
 java -jar trimmomatic-0.39.jar PE -phred33 SRR26624132_1.fastq SRR26624132_2.fastq trim1_paired.fastq trim1_unpaired.fastq trim2_paired.fastq trim2_unpaired.fastq ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
 ```
 ### Step 4: Genome Assembly
 Use Velvet for de novo genome assembly:
-
+- [Velvet](http://www.ebi.ac.uk/~zerbino/velvet/)
+or
 Install Velvet (For macOS): brew install velvet
 Install Velvet (For Ubuntu): sudo apt-get install velvet
 ```bash
@@ -33,7 +36,7 @@ velvetg ./velvet_output -clean yes -exp_cov 21 -cov_cutoff 2.81 -min_contig_lgth
 ```
 ### Step 5: BLAST Analysis
 Use BLAST to compare assembled contigs with a reference genome:
-
+- [blast executables](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)
 Install BLAST: brew install blast or sudo apt-get install ncbi-blast+
 ```bash
 blastp -query ./velvet_output/contigs.fa -db ref_genome -out blast_result.txt -evalue 1e-04 -outfmt 6 -max_target_seqs 5 -num_threads 8
@@ -44,4 +47,4 @@ Retrieve top gene IDs from BLAST results:
 ```bash
 cut -f 2 blast_result.txt | sort | uniq | head -n 10 > top_gene_ids.txt
 ```
-Annotate genes using UniProt and PANTHER databases. Visit the PANTHER website and upload the gene list for functional annotation.
\ No newline at end of file
+Annotate genes using UniProt and PANTHER databases. Visit the [PANTHER](https://www.pantherdb.org/) website and upload the gene list for functional annotation.
\ No newline at end of file