P.falciparum genome assemblies from the GAMCC study

This data accompanies the paper: Forster AJ et al, "Paralogous mutations in the Plasmodium falciparum surface anion channel associate with reduced protection due to sickle haemoglobin", to appear shortly. A preprint is available on medRxiv. Enclosed are genome assemblies of P.falciparum parasites from infections of Gambian children from the GAMCC study, sequenced as part of a trial of fragmentation processes at the Centre for Human Genetics, University of Oxford. The two samples are `GAM958463` and `GAM249017`; both were assembled from PacBio reads generated on the SequelIIe platform.   Enclosed are genome assemblies of P.falciparum parasites from infections of Gambian children from the GAMCC study, sequenced as part of a trial of fragmentation processes at the Centre for Human Genetics, University of Oxford.. The two samples are GAM958463 and GAM249017; both were assembled from PacBio reads generated on the SequelIIe platform. Assembly details GAM958463 was assembled from 211,271 HiFi reads with a mean length of 8,089bp, amounting to ~74x genome coverage. It has 37 contigs. GAM249017 was assembled from 213,889 HiFi reads with a mean length of 7,750bp, amounting to ~72x coverage. It has 55 contigs. Both assemblies were generated using hifiasm with default parameters. Following assembly, we used order-orient with the Pf3D7_v3 reference sequence, to orient and re-name each contig to match the reference sequence. For each sample, the files enclosed are: [sample id].gfa.gz Tthe output [GFA file](gfa-spec.github.io) from `hifiasm` representing primary contigs. It can be viewed in [`BandageNG`](github.com) or other software. [sample id].oriented.fa.gz A FASTA file representing the output file of the order-orient tool, containing the contigs aligned/oriented and renamed to match Pf3D7_v3 reference assembly chromosomes. The contig naming scheme is: [sample id]_[chromosome]. Where multiple contigs align to the same reference chromosome, additional contigs are numbered as [sample id]_[chromosome]_[index], with an index starting at 2. The contig names are also decorated with the following tags: ZS: the name of the source contig in the .gfa.gz file ZL: the length in bp of the contig ZO: the orientation - if this is -, the sequence in this file is the reverse complement of that in the gfa.gz file. ZR: the `Pf3D7_v3` reference contig to which this contig best aligned (from `minimap2`) ZA: the length of the primary alignment of this contig to the reference sequence in ZR (from minimap2). AS: the alignment score of this contig to the sequence in ZR (from minimap2). NM: the edit distance of the alignment (from minimap2).