PANDAseq pipeline

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

 (5)
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)[45]. 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 […]

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

[…] remove adapters using the sequences packaged with the a5-miseq assembly pipeline (coil et al., 2015). low quality and short sequences (<75 nt) were discarded. sequences were then assembled using pandaseq (masella et al., 2012); unassembled pairs were retained. de novo assembly was conducted on the assembled and unassembled pairs using megahit (li d. et al., 2015) and contigs shorter than 200 […]

2017
PMCID: 5420135
PMID: 28476135
DOI: 10.1186/s40168-017-0265-7

[…] for pcr products and dna extractions repeated as necessary. sequencing reads were analyzed using custom perl scripts [24]. briefly, sequences with low quality reads were trimmed using cutadapt [25]. pandaseq was used to assemble paired-end reads [26]. operational taxonomic units (otus) were picked using abundantotu+ for otus with ≥97% identity [27]. the rdp classifier (version 2.2) was used […]

2017
PMCID: 5432662
PMID: 28540183
DOI: 10.1016/j.gdata.2017.05.007

[…] cv. jro-524, and shotgun libraries were prepared followed by paired-end sequencing on an illumina miseq platform, generating 2 × 250 bp overlapping reads. the cleaned sequence reads were merged with pandaseq and assembled de novo using newbler software. genes were predicted by fgenesh and annotated using blastx against the ncbi non-redundant protein database. we used symap for pairwise synteny […]

2016
PMCID: 5069773
PMID: 27822538
DOI: 10.1128/mSystems.00024-16

[…] deeper sequencing depth per library., for each sequenced library, adaptors were removed with trimmomatic (97) v. 0.27 (parameters: illuminaclip::2:40:15) and paired-end reads were then joined with pandaseq (98) v. 2.4 (parameters: -f 6 −t 0.32). the ends of joined reads and reads unable to be paired with quality scores of <5 were clipped, and sequences shorter than 40 bases or made […]

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

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