Leishmania infantum (strain LLM-2413): Illumina sequencing reads and genomic pseudo-assembly

This strain (MHOM/ES/2018/LLM-2413) was isolated from a patient with leishmaniasis at Centro Nacional de Microbiología (WHO Collaborating Centre for Leishmaniasis, Instituto de Salud Carlos IIII, Madrid, Spain). Total DNA was used for short-read whole-genome sequencing at the Centro Nacional de Análisis Genómico (CNAG-CRG) using the Illumina HiSeq platform, generating paired-end reads of 100 bp in length. A total of 41,108,278 reads were obtained, and they are provided in this dataset (LiL7_1.fastq and LiL7_2.fastq).

            The reads were aligned against the L. infantum (JPCM5 strain) reference genome [1] with the BWA-MEM software [2], using default parameters, and post-processed with Picard tools (https://broadinstitute.github.io/picard/). Variant discovery and genotyping were performed using the Genome Analysis Toolkit (GATK) [3]. Finally, a reference-guided consensus genome (pseudo-assembly) was then generated by mapping the variants to the reference genome (JPCM5 strain)  using bcftools consensus [4]. Regions with zero coverage were subsequently masked using bedtools maskfasta [5], and their positions in the pseudo-assemblies were marked by N. A Fasta file with the sequence of the 36 chromosomes is provided (LiL7_consensus_DEF.fasta).

References

1. Gonzalez-de la Fuente, S.; Peiro-Pastor, R.; Rastrojo, A.; Moreno, J.; Carrasco-Ramiro, F.; Requena, J.M.; Aguado, B. (2017) Resequencing of the Leishmania Infantum (Strain JPCM5) Genome and de Novo Assembly into 36 Contigs. Sci Rep 7:18050, doi:10.1038/s41598-017-18374-y.

2. Li, H.; Durbin, R. (2009) Fast and Accurate Short Read Alignment with Burrows-Wheeler Transform. Bioinformatics 25:1754–1760, doi:10.1093/bioinformatics/btp324.

3. McKenna, A.; Hanna, M.; Banks, E.; Sivachenko, A.; Cibulskis, K.; Kernytsky, A.; Garimella, K.; Altshuler, D.; Gabriel, S.; Daly, M.; et al. (2010) The Genome Analysis Toolkit: A MapReduce Framework for Analyzing next-Generation DNA Sequencing Data. Genome Res.  20:1297–1303, doi:10.1101/GR.107524.110.

4. Danecek, P.; Bonfield, J.K.; Liddle, J.; Marshall, J.; Ohan, V.; Pollard, M.O.; Whitwham, A.; Keane, T.; McCarthy, S.A.; Davies, R.M. (2021) Twelve Years of SAMtools and BCFtools. Gigascience 10:giab008, doi:10.1093/GIGASCIENCE/GIAB008.

5. Quinlan, A.R.; Hall, I.M. (2010) BEDTools: A Flexible Suite of Utilities for Comparing Genomic Features. Bioinformatics  26: 841–842, doi:10.1093/bioinformatics/btq033.