For release 1.0.4 and eariler

For paired-end correction, it assumes that each read is next to its mate read (i.e. interleaved). In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3 are paired and so on. Note that there must be no blank lines in both files.

1. Specify the "-paired" or "-inorder" option to perform error correction for paire-end reads.
2. The paired-end correction keeps reads outputed in the same order with the input.
3. If the paired reads are stored in two separate FASTA/FASTQ files, the bundled Perl scripts can be used to merge the two files into a single one with interleaved paired-end reads. Subsequently, this new file is used as input of Musket.
   • To generate a single file storing the interleaved paired-end reads, type:
     • shuffleSequences_fasta.pl reads_1.fa reads_2.fa output.fa
     • shuffleSequences_fastq.pl reads_1.fa reads_2.fq output.fq
   • To extract the error-corrected interleaved paired-end reads from the output file, type:
     • extractSequences_fasta.pl input.fa reads_1.fa reads_2.fa
     • extractSequences_fastq.pl input.fq reads_1.fa reads_2.fq