The SRA houses DNA sequences, and so for nucleotide:nucleotide searches we use bowtie2 to compare the fasta file of DNA sequences you upload against the set of SRA IDs of the metagenomes that you choose to search. We convert the output to binary sequence alignment format and provide you with a compressed zip file containing both the bam and bam index files for your downstream processing.
The command that we currently use for bowtie2 is:
bowtie2 -p 6 -q --no-unal -x SRAMG -U DATA | samtools view -bS - | samtools sort - OUTPUT
SRAMG is one of our preprocessed metagenomes, and DATA is the fasta file that you upload.
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