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Protocols

PANDAseq specifications

Information


Unique identifier OMICS_05255
Name PANDAseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Publication for PANDAseq

PANDAseq citations

 (184)
library_books

Climate driven shifts in sediment chemistry enhance methane production in northern lakes

2018
Nat Commun
PMCID: 5935729
PMID: 29728566
DOI: 10.1038/s41467-018-04236-2

[…] sequenced on an Illumina MiSeq using the prokaryote primers Pro 341 F (5′-CCTACGGGNBGCASCAG-3′) and Pro805R (5′-GACTACNVGGGTATCTAATCC-3′) by Metagenome Bio Inc. Resulting sequences were merged using Pandaseq and further quality filtered and taxonomy was assigned from the Green Genes database using Usearch v8.1.1861 and QIIME, respectively–. Data were analyzed in R with the Phyloseq package, and a […]

library_books

Human Activity Determines the Presence of Integron Associated and Antibiotic Resistance Genes in Southwestern British Columbia

2018
Front Microbiol
PMCID: 5938356
PMID: 29765365
DOI: 10.3389/fmicb.2018.00852

[…] n 0.32 () was used to remove adapters using the sequences packaged with the A5-Miseq assembly pipeline (). Low quality and short sequences (<75 nt) were discarded. Sequences were then assembled using PandaSeq (); unassembled pairs were retained. De novo assembly was conducted on the assembled and unassembled pairs using MEGAHIT () and contigs shorter than 200 nt were discarded. Nucleotide sequence […]

call_split

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations

2018
Front Microbiol
PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792
call_split See protocol

[…] 16S rRNA gene reads were initially screened for low quality bases and short read lengths (), paired reads were merged using PANDAseq (), de-multiplexed, trimmed of artificial barcodes and primers, and assessed for chimeras using UCHIME in de novo mode, as implemented in Quantitative Insights Into Microbial Ecology (QIIME; […]

library_books

How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?

2018
Front Microbiol
PMCID: 5915629
PMID: 29720967
DOI: 10.3389/fmicb.2018.00651

[…] The resulting read pairs were quality filtered with Sickle (), merged with Pandaseq () and denoised with BayesHammer (). The sequences were classified with naive Bayesian classifier () with SILVA Seed v.123 database then bacterial and non-bacterial ones were separated.In cas […]

library_books

Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta and mucosa associated microbiota in pigs

2018
Sci Rep
PMCID: 5897541
PMID: 29651010
DOI: 10.1038/s41598-018-24043-5

[…] Bioinformatic analyses were performed as described by Derakhshani et al.. In brief, the PANDAseq assembler was used to merge overlapping paired-end Illumina fastq files. All the sequences with low quality base calling scores as well as those containing uncalled bases (N) in the overlappi […]

call_split

Meta scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non rhizosphere soil bacterial communities

2018
Sci Rep
PMCID: 5893626
PMID: 29636506
DOI: 10.1038/s41598-018-24253-x
call_split See protocol

[…] ecause it can be completely covered by paired-end Illumina HiSeq reads (2 × 100 nt). The sequenced paired-end reads were demultiplexed and quality filtered using in-house scripts, and assembled using PandaSeq. Filtered reads were clustered into OTUs at the 97% similarity threshold using QIIME v.1.7.0 and the gg_13_8 database from Greengenes as a reference. The OTUs per sample were then normalized […]

Citations

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PANDAseq institution(s)
Department of Biology, University of Waterloo, Waterloo, ON, Canada

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