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Diamond diamond blastx -d nr -q reads.fna -o matches.m8 DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. Show
Diamond makedb diamond makedb --in nr.faa -d nr DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. The command above sets up a reference database for DIAMOND. Show
blastn blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] search nucleotide database using a nucleotide query Show
tblastx tblastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] search translated nucleotide database using a translated nucleotide query Show
blastp blastp -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] search protein database using a protein query Show
tview samtools tview [-p chr:pos] [-s STR] [-d display] <in.sorted.bam> [ref.fasta] Text alignment viewer (based on the ncurses library). In the viewer, press `?' for help and press `g' to check the alignment start from a region in the format like `chr10:10,000,000' or `=10,000,000' when viewing the same reference sequence. Show
blastx blastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] search protein database using a translated nucleotide query Show
tblastn tblastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] search translated nucleotide database using a protein query Show