Whole-genome sequencing of Leishmania tarentolae

Paired-ends sequencing libraries were prepared from L. tarentolae genomic DNA with the Nextera DNA sample prep kit and sequenced on an Illumina HiSeq platform with 101-nucleotides paired-ends reads. Sequence reads were aligned to the L. tarentolae Parrot TarII PacBio genome assembly [22 (link)] using bwa-mem [23 (link)]. Read duplicates were marked using Picard and GATK was applied for single nucleotide variants and small insertions or deletions discovery [24 (link)]. Copy numbers variations were derived from read depth coverage as described earlier [25 (link)].

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Roy G., Bhattacharya A., Leprohon P, & Ouellette M. (2021). Decreased glutamate transport in acivicin resistant Leishmania tarentolae. PLoS Neglected Tropical Diseases, 15(12), e0010046.

Publication 2021

DNA sample prep kit HiSeq platform

Copy numbers variations Deletions Genome Insertions Nucleotide Parrot

Corresponding Organization : Université Laval

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Variable analysis

independent variables

Paired-ends sequencing libraries prepared from L. tarentolae genomic DNA with the Nextera DNA sample prep kit

dependent variables

Single nucleotide variants and small insertions or deletions
Copy numbers variations

control variables

Sequencing reads aligned to the L. tarentolae Parrot TarII PacBio genome assembly

controls

No positive or negative controls were explicitly mentioned in the provided information.

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