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