SeqPrep statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SeqPrep
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Tool usage distribution map

This map represents all the scientific publications referring to SeqPrep per scientific context
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Associated diseases

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Popular tool citations

chevron_left Adapter trimming Read elongation chevron_right
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Protocols

SeqPrep specifications

Information


Unique identifier OMICS_01092
Name SeqPrep
Software type Application/Script
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, Python, Shell (Bash)
License MIT License
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

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Documentation


SeqPrep citations

 (142)
library_books

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

2018
Sci Rep
PMCID: 5935716
PMID: 29728615
DOI: 10.1038/s41598-018-25338-3

[…] were generated by Illumina base calling software CASAVAv1.8.2 (http://support.illumina.com/sequencing/sequencing_software/casava.ilmn), and sequences containing adaptors or primers were identified by SeqPrep (https://github.com/jstjohn/SeqPrep). Sickle (https://github.com/najoshi/sickle) was applied to conduct reads trimming with default parameters to obtain clean data for this study. In addition, […]

library_books

Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella

2018
Front Microbiol
PMCID: 5928149
PMID: 29740401
DOI: 10.3389/fmicb.2018.00728

[…] The sequence analysis was conducted using the QIIME 1.9.0 package (). Paired end reads were assembled using SeqPrep. Chimeric sequences were identified with Chimera Slayer (). OTU picking was performed using the pick_open_reference_otus.py protocol with at least 97% identity per OTU and annotation was condu […]

library_books

Aggressive natural killer cell leukemia mutational landscape and drug profiling highlight JAK STAT signaling as therapeutic target

2018
Nat Commun
PMCID: 5908809
PMID: 29674644
DOI: 10.1038/s41467-018-03987-2

[…] SRA accession identifiers for public datasets are listed in Supplementary Data . Raw reads were merged with SeqPrep. Resulting paired reads were trimmed of B blocks in the quality scores from the end of the read. Trimmed reads shorter than 36 base pairs were removed. Reads were aligned using the Burrows–Whe […]

library_books

A large scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition

2018
Sci Rep
PMCID: 5893548
PMID: 29636512
DOI: 10.1038/s41598-018-23989-w

[…] Raw fastq files were assembled, quality-filtered, and analyzed using the default settings [join_paired_ends.py (-m SeqPrep); split_libraries_fastq.py (-q 19)] in QIIME (version 1.8.0 for Macintosh), as described in our previous work, and others. After quality control, the remaining high-quality sequences were binn […]

call_split

Liver Transcriptome and miRNA Analysis of Silver Carp (Hypophthalmichthys molitrix) Intraperitoneally Injected With Microcystin LR

2018
Front Physiol
PMCID: 5902739
PMID: 29692738
DOI: 10.3389/fphys.2018.00381
call_split See protocol

[…] In order to ensure the accuracy of the follow-up experimental analysis, raw data was screened by software SeqPrep and Sickle to acquire a clean data. All clean data were subjected to de-novo assembly for further analysis using Trinity. […]

call_split

Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra

2018
Front Microbiol
PMCID: 5891625
PMID: 29666616
DOI: 10.3389/fmicb.2018.00629
call_split See protocol

[…] re deposited at the SRA and are available under the project ID SRP128106. The sequence analysis was conducted using the QIIME 1.9.0 package (RRID:SCR_008249) (). Paired-end reads were assembled using SeqPrep (RRID:SCR_013004). Chimeric sequences were identified with ChimeraSlayer (RRID:SCR_013283) () and verified manually before removal from the data set. If a putative chimera was present in at le […]


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