This information is then followed by the count of singletons (encoded as a 32-bit unsigned integer) and a bitstream containing all singleton reads, sorted reverse lexicographically and 2-bit encoded.
These reads were sorted into separate files according to their barcode, with the barcode removed and the remainder of the sequence trimmed to 64 bases (including the initial CWGC).
The resulting sequencing reads were sorted according to the genome segments to which they related and were subsequently assembled into one contig (i.e., a set of overlapping sequencing reads) per segment with the GS FLX sequence assembly software newbler (version 2.3; Roche).
Mapped reads were sorted and indexed with samtools [ 18].
Mapped reads were sorted and indexed using SAMtools [ 120].
Resulting mapped reads were sorted and converted to BAM format using samtools v0.1.19.
Mapped reads were sorted and indexed using SAMtools (Li et al., 2009).
Sequencing reads were sorted into separate files according to their barcode, and linker sequences were removed.
Aligned reads were sorted, indexed and compressed into the BAM format for easy storage and usage in downstream analysis.
When all source k-mershave been read, the sorted runs are merged and the main succinct bitmap is constructed.
