StreamingTrim protocols

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StreamingTrim specifications

Information


Unique identifier OMICS_05196
Name StreamingTrim
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Alessio Mengoni <>

Publication for StreamingTrim

StreamingTrim in pipelines

 (3)
2017
PMCID: 5481584
PMID: 28642378
DOI: 10.1128/genomeA.00565-17

[…] sequencing system (illumina, inc., san diego, ca). the fastqc software package version 0.52 () was used to evaluate the quality of the obtained read pairs, and poor-quality bases were removed using streamingtrim (). assembly was performed using the spades 3.5 software (), with k-mer lengths of 21, 33, and 55, generating 21 contigs. those having a length shorter than 200 nucleotides were removed […]

2017
PMCID: 5578044
PMID: 28758937
DOI: 10.3390/ijms18081654

[…] deposited in the national center for biotechnology information (ncbi) “sequence read archive” (sra) under the project accession prjna316056. , sequence quality was ensured by trimming reads using streamingtrim 1.0 [], with a quality cutoff of 20. bowtie2 [] was used to screen out human-derived sequences from metagenomic data with the latest version of the human genome available in the ncbi […]

2015
PMCID: 4395073
PMID: 25792047
DOI: 10.1128/genomeA.00109-15

[…] high-quality contigs (). the 454 reads (191,539 reads) have been converted to the fastq format using the seq_crumbs package (version 0.1.8; http://bioinf.comav.upv.es/seq_crumbs/) and trimmed using streamingtrim (version 1.0) (). both 454 and pacbio reads quality has been checked using fastqc (version 0.10.1) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). the pacbio reads (118,344 […]


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StreamingTrim in publications

 (7)
PMCID: 5578044
PMID: 28758937
DOI: 10.3390/ijms18081654

[…] deposited in the national center for biotechnology information (ncbi) “sequence read archive” (sra) under the project accession prjna316056. , sequence quality was ensured by trimming reads using streamingtrim 1.0 [], with a quality cutoff of 20. bowtie2 [] was used to screen out human-derived sequences from metagenomic data with the latest version of the human genome available in the ncbi […]

PMCID: 5073339
PMID: 27767072
DOI: 10.1038/srep35790

[…] that were used for ipcr. the sequences have been submitted to the mg-rast database under project accession number 9119., adapters were removed using cutadapt and the reads were quality trimmed using streamingtrim with the option -q 20. quality trimmed reads were mapped using bwa with the bwa mem -command with default parameters against the card antibiotic resistance database. bacterial 16s rrna […]

PMCID: 4966461
PMID: 27469957
DOI: 10.1128/genomeA.00728-16

[…] (university of udine, italy). a total of 11,007,120 and of 12,698,315 reads were obtained for pseudomonas sp. taa207 and pseudomonas sp. tad18, respectively. low-quality sequences were trimmed with streamingtrim (), and the remaining were assembled with spades genome assembler version 3.6.1 (). only contigs longer than 1,000 bp were embedded in the final version of the draft genomes, […]

PMCID: 4935691
PMID: 27458451
DOI: 10.3389/fmicb.2016.01060

[…] al., )., raw sequences were clustered into “operation taxonomic units” (otus) following the uparse pipeline as previously described (bacci et al., ,). a pre-processing step was also included using streamingtrim (bacci et al., ), to remove low-quality reads that can generate errors in downstream analyses. read pairs were merged using pandaseq assembler with default settings (masella et al., ). […]

PMCID: 4927098
PMID: 27355625
DOI: 10.1371/journal.pone.0156807

[…] prjna290694., amplicon sequences were demultiplexed using mothur [], discarding those with mismatches in the barcode, primers, linkers or spacers. a first quality check step was performed using streamingtrim [] to remove ambiguous base calls (phred’s quality score < 25) and convert sequences into fastq format. filtered sequences were processed following the uparse pipeline included […]


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StreamingTrim institution(s)
Department of Biology, University of Florence, Firenze, Italy; Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo, Roma, Italy
StreamingTrim funding source(s)
Supported by a fellowship from MIPAAF and by intramural funding of the university of Florence.

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