Align

Diamond
Function: DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
Usage: diamond blastx -d nr -q reads.fna -o matches.m8
blastn
Function: search nucleotide database using a nucleotide query
Usage: blastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
Diamond makedb
Function: 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.
Usage: diamond makedb --in nr.faa -d nr
samtools
Function: 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.
Usage: samtools tview [-p chr:pos] [-s STR] [-d display] <in.sorted.bam> [ref.fasta]
blastx
Function: search protein database using a translated nucleotide query
Usage: blastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
blastp
Function: search protein database using a protein query
Usage: blastp -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
tblastx
Function: search translated nucleotide database using a translated nucleotide query
Usage: tblastx -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]
tblastn
Function: search translated nucleotide database using a protein query
Usage: tblastn -query input_reads.fasta -db input_reads_db -out blastn_output.alignments [options]