| 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. |
| blastn |
blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] |
search nucleotide database using a nucleotide query |
| blastx |
blastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] |
search protein database using a translated nucleotide query |
| blastp |
blastp -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] |
search protein database using a protein query |
| samtools |
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. |
| tblastx |
tblastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] |
search translated nucleotide database using a translated nucleotide query |
| 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. |
| tblastn |
tblastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options] |
search translated nucleotide database using a protein query |