Pipeline publication

[…] lin strain) annotation as a reference. Given the importance of maintaining current L. infantum gene ID names, OrthoMCL, BLAST searches were performed to assign correspondences between the Companion annotated genes and current L. infantum gene names (version 9, TriTrypDB.org). These additional data were combined with those provided by Companion annotation into a GFF3 file using an in-house Python script. Finally, the GFF3 file was manually curated to resolve ambiguous annotations and to name those new genes uncovered in the new assembled L. infantum genome. The complete annotation of the new genome (GFF3 file) is provided in the Supplementary file  in Excel format., Synteny was evaluated via SyMAP and progressive MAUVE algorithms using current L. infantum (v.9, GeneDB.org) and L. major genomes as reference. Synteny graphs were prepared by genoPlotR, and provided as Supplementary Figures –., The Illumina paired ends reads (FASTQ) and PacBio bax.h5 reads of L. infantum (JPCM5 strain) generated for this study are available at The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/). Also, the assembled genome sequence and an annotation file were uploaded. All data have been deposited under the Study accession number PRJEB20254 and Study unique name: ena-STUDY-CBMSO-04-04-2017-10:39:08:689–498. The new L. infantum genome sequence will also be available at the Leish-ESP web site (https://leishseq.neocities.org/)., , Electronic supplementary material , Supplementary information accompanies this paper at 10.1038/s41598- […]

Pipeline specifications

Software tools SyMAP, Mauve, genoPlotR
Databases ENA TriTrypDB GeneDB
Organisms Leishmania, Toxoplasma gondii, Homo sapiens, Leishmania major, Leishmania braziliensis
Diseases Gastrointestinal Diseases, Euglenozoa Infections, Skin Diseases, Infectious, Leishmaniasis