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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS, Windows|
|License||GNU General Public License version 2.0|
No version available
Publication for PANDAseq
Climate driven shifts in sediment chemistry enhance methane production in northern lakes
[…] 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 […]
Human Activity Determines the Presence of Integron Associated and Antibiotic Resistance Genes in Southwestern British Columbia
[…] 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 […]
Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations
[…] 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; […]
How Does Salinity Shape Bacterial and Fungal Microbiomes of Alnus glutinosa Roots?
[…] 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 […]
Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta and mucosa associated microbiota in pigs
[…] 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 […]
Meta scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non rhizosphere soil bacterial communities
[…] 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 […]
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