LGAAP:
            <i>Leishmaniinae</i>
            Genome Assembly and Annotation Pipeline

Almutairi, Hatim; Urbaniak, Michael D.; Bates, Michelle; Jariyapan, Narissara; Kwakye-Nuako, Godwin; Thomaz-Soccol, Vanete; Al-Salem, Waleed S.; Dillon, Rod J.; Bates, Paul A.; Gatherer, Derek

doi:10.1128/mra.00439-21

Cited by 8 publications

(7 citation statements)

References 22 publications

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“…Links to both published and unpublished software used are provided in Table 2 . We created public GitHub and Zenodo repositories for the analysis pipeline 29 , 30 .…”

Section: Methodsmentioning

confidence: 99%

“…To make sure that all assemblies and annotations are reproducible by future investigators, the entire process from obtaining the SRAs 49 – 91 to the annotation assignments 92 – 97 has been made available 29 using Snakemake 98 . This Snakemake pipeline ought to be easily adaptable to the sequencing of further similar parasite genomes, throughout the parasitology community 30 .…”

Section: Methodsmentioning

confidence: 99%

“…The Snakemake analyses pipeline was deposited at GitHub and Zenodo repositories 29 , 30 . Links to software used as well as relevant conda and docker containers are given in Table 2 .…”

mentioning

confidence: 99%

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Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

et al. 2021

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We provide the raw and processed data produced during the genome sequencing of isolates from six species of parasites from the sub-family Leishmaniinae: Leishmania martiniquensis (Thailand), Leishmania orientalis (Thailand), Leishmania enriettii (Brazil), Leishmania sp. Ghana, Leishmania sp. Namibia and Porcisia hertigi (Panama). De novo assembly was performed using Nanopore long reads to construct chromosome backbone scaffolds. We then corrected erroneous base calling by mapping short Illumina paired-end reads onto the initial assembly. Data has been deposited at NCBI as follows: raw sequencing output in the Sequence Read Archive, finished genomes in GenBank, and ancillary data in BioSample and BioProject. Derived data such as quality scoring, SAM files, genome annotations and repeat sequence lists have been deposited in Lancaster University’s electronic data archive with DOIs provided for each item. Our coding workflow has been deposited in GitHub and Zenodo repositories. This data constitutes a resource for the comparative genomics of parasites and for further applications in general and clinical parasitology.

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“…Links to both published and unpublished software used are provided in Table 2 . We created public GitHub and Zenodo repositories for the analysis pipeline 29 , 30 .…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

et al. 2021

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“…The analysis workflow for assembly and annotation was performed using Snakemake ( 15 ) and is available online for reproducibility purposes ( https://github.com/hatimalmutairi/LGAAP ), including the software versions and parameters used ( 16 ). Figure 1 compares our assembly with other complete genomes.…”

Section: Announcementmentioning

confidence: 99%

Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43

Almutairi

Urbaniak

Bates

et al. 2021

Microbiol Resour Announc

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Porcisia hertigi is a parasitic kinetoplastid first isolated from porcupines ( Coendou rothschildi ) in central Panama in 1965. We present the complete genome sequence of P. hertigi , isolate C119, strain LV43, sequenced using combined short- and long-read technologies. This complete genome sequence will contribute to our knowledge of the parasitic genus Porcisia .

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“…Despite concerns about the genetic variation of L. orientalis and their public health impacts, genomic information of multiple L. orientalis isolates has gained attention. To date, three major genome sequencing platforms (Illumina, PacBio, and Oxford Nanopore) have been used to create the complete genomic data of several Leishmania species, including the genome of L. major strain Friedlin [ 31 , 42 , 43 , 44 ], L. infantum strain JPCM5 [ 33 , 42 ], L. martiniquensis strain LSCM1 [ 45 , 46 , 47 ], and a recent L. orientalis strain LSCM4 isolated from the northern province of Thailand [ 46 , 47 , 48 ], in exchange for considerable cost invested in the genome project. Questions have arisen on whether the new Leishmania species shall have their whole genomes decoded using all techniques at first glance.…”

Section: Introductionmentioning

confidence: 99%

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

Anuntasomboon

Siripattanapipong

Unajak

et al. 2022

Biology

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Background: Leishmania orientalis (formerly named Leishmania siamensis) has been neglected for years in Thailand. The genomic study of L. orientalis has gained much attention recently after the release of the first high-quality reference genome of the isolate LSCM4. The integrative approach of multiple sequencing platforms for whole-genome sequencing has proven effective at the expense of considerably expensive costs. This study presents a preliminary bioinformatic workflow including the use of multi-step de novo assembly coupled with the reference-based assembly method to produce high-quality genomic drafts from the short-read Illumina sequence data of L. orientalis isolate PCM2. Results: The integrating multi-step de novo assembly by MEGAHIT and SPAdes with the reference-based method using the L. enriettii genome and salvaging the unmapped reads resulted in the 30.27 Mb genomic draft of L. orientalis isolate PCM2 with 3367 contigs and 8887 predicted genes. The results from the integrated approach showed the best integrity, coverage, and contig alignment when compared to the genome of L. orientalis isolate LSCM4 collected from the northern province of Thailand. Similar patterns of gene ratios and frequency were observed from the GO biological process annotation. Fifty GO terms were assigned to the assembled genomes, and 23 of these (accounting for 61.6% of the annotated genes) showed higher gene counts and ratios when results from our workflow were compared to those of the LSCM4 isolate. Conclusions: These results indicated that our proposed bioinformatic workflow produced an acceptable-quality genome of L. orientalis strain PCM2 for functional genomic analysis, maximising the usage of the short-read data. This workflow would give extensive information required for identifying strain-specific markers and virulence-associated genes useful for drug and vaccine development before a more exhaustive and expensive investigation.

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LGAAP: Leishmaniinae Genome Assembly and Annotation Pipeline

Cited by 8 publications

References 22 publications

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

Chromosome-scale genome sequencing, assembly and annotation of six genomes from subfamily Leishmaniinae

Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43

Making the Most of Its Short Reads: A Bioinformatics Workflow for Analysing the Short-Read-Only Data of Leishmania orientalis (Formerly Named Leishmania siamensis) Isolate PCM2 in Thailand

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