PANDAseq protocols

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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 in pipelines

 (51)
2018
PMCID: 5759273
PMID: 29316977
DOI: 10.1186/s40168-017-0381-4

[…] curve was created using tenfold serial dilutions from concentrations of 3.99 × 101 to 3.99 × 107 copies per milliliter., paired-end reads were trimmed using trimmomatic [], assembled together using pandaseq [], and the resulting sequences were subjected to filtering, denoising, and chimera removal within qiime []. otu picking at 97% identity was accomplished with a combination of ninja_ops [] […]

2018
PMCID: 5765012
PMID: 29323168
DOI: 10.1038/s41598-017-18777-x

[…] scores with sickle (https://github.com/najoshi/sickle) followed by error correction with bayeshammer., the resulting quality trimmed and error corrected paired-end sequences were assembled using pandaseq software. this approach has been shown to reduce the substitution error rates by ~93% in illumina miseq sequence data. further sequence processing steps were performed on mothur pipeline. […]

2018
PMCID: 5773227
PMID: 29346435
DOI: 10.1371/journal.ppat.1006796

[…] 4 bases of r2 reads were trimmed using fastx_trimmer from the fastx toolkit (v. 0.0.13; http://hannonlab.cshl.edu/fastx_toolkit/). overlapping paired-end reads were merged into a single read using pandaseq (v. 2.9)[]. merged reads were processed using filter_fastq_by_primerid_length.pl to identify and extract the primerid from each read, with options—post ca—removepost, and place the primerid […]

2018
PMCID: 5796797
PMID: 29303478
DOI: 10.7554/eLife.32724.036

[…] efficiency, the same phage dilutions were used for all experiments., after applying a low-pass filter, reads were trimmed using cutadapt v. 1.14 () and paired-end overlapping reads were merged using pandaseq () for error correction. reads were mapped to the ms2 genome with bowtie2 v2.3.0 () using the ‘very-sensitive’ option and de-duplicated based on the dual-umi (). feature counts were obtained […]

2018
PMCID: 5797768
PMID: 29445360
DOI: 10.3389/fmicb.2018.00032

[…] taxonomy analysis was carried out on qiime. raw sequence data of this study have been deposited to the ncbi sequence read archive with accession no. srp127379., sample reads were assembled by using pandaseq (v2.7), trimmomatic (v0.30), and usearch (v8.0). sequences shorter than 400 bp or containing homopolymers and ambiguous bases were removed, and adapter/index sequences were trimmed. […]


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PANDAseq in publications

 (201)
PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] steps. briefly, quality control (qc) of mirna sequencing data was performed using fastqc before and after adaptor trimming with trimmomatic (). then, the paired-end reads were assembled using pandaseq and aligned to the hg38 genome assembly using bowtie2 (, ). finally, the total mature mirna counts were generated with htseq (). we removed 7 samples (s01, s02, s03, s36, s40, s41, s43) due […]

PMCID: 5938356
PMID: 29765365
DOI: 10.3389/fmicb.2018.00852

[…] () 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 […]

PMCID: 5928236
PMID: 29740420
DOI: 10.3389/fmicb.2018.00792

[…] the institute for genome sciences (), described in detail elsewhere (,)., 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; […]

PMCID: 5915629
PMID: 29720967
DOI: 10.3389/fmicb.2018.00651

[…] using hplc-purified versions of forward and reverse primers as well as reverse-complement of the reverse primer (table )., 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., […]

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

[…] (row normalize length transformation, past, version 2.17) was used to for generating the clustering heat map., 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) […]


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

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