For SRA accessions Magic-BLAST determines whether reads are paired and maps them appropriately.

For reads in FASTA and FASTQ files paired reads can either be in a single file, or two files.

Single file

For paired reads presented as successive entries in a single FASTA or FASTQ file, i.e. read 1 and 2 of fragment 1, then read 1 and 2 of fragment 2, etc., simply add the parameter -paired:

magicblast -query reads.fa -db genome -paired


magicblast -query reads.fastq -db genome -paired -infmt fastq
Two files

For paired reads presented in two parallel files, use these options:

magicblast -query reads.fa -query_mate mates.fa -db genome


magicblast -query reads.fastq -query_mate mates.fastq -db genome -infmt fastq