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