Quality control, sequence alignment and gene expression counts were obtained using MAP-R seq workflow [28].
Recent advances in numerical optimization techniques have made it possible to design high quality control sequences that are robust against the various experimental uncertainties [20, 27, 32, 49, 52].
The quality control sequences were then searched against all collected BAC end sequences with BLAST program.
The reads and their mates that mapped onto run quality control sequences (PhiX genome) were removed.
As a measure of quality control, sequence segments of individuals presenting singletons or ambiguous polymorphisms were reamplified and resequenced.
PHRED, PHRAP, and CONSED were used with default parameters for base calling and quality control, sequence assembly, and contig ordering, respectively.
After quality control, sequence error rate was estimated as the percentage of single-base mutations in the rpl32- trnL region within individuals and was found to be approximately 0.13% (see Methods).
10 WGS on the Illumina HiSeq2500 platform (Illumina Inc., San Diego, CA) will yield up to 130× coverage of the P. falciparum genome, and data processing will include quality control, sequence alignment, and variant discovery based on the P. falciparum 3D7 reference sequence.
155 quality controlled sequences were submitted in FASTA format to the Stanford HIV Database Calibrated Population Resistance tool (CPR) [ 10] in order to derive an unambiguous and stable measure of TDR [ 11].
To estimate the inclusivity of the set of assemblies, we aligned the post-quality-control sequencing reads to the assembled contigs with bowtie2 [ 11] version 2.2.4.
After this quality control, the sequencing reads were mapped to the reference sequence, resulting in a higher percentage of mapped reads for the Illumina MiSeq.
