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.
- Specify the "-paired" or "-inorder" option to perform error correction for paire-end reads.
- The paired-end correction keeps reads outputed in the same order with the input.
- 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