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Scythe specifications

Information


Unique identifier OMICS_01091
Name Scythe
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, R, Shell (Bash)
License MIT License
Computer skills Advanced
Stability Stable
Requirements
Zlib
Maintained Yes

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Maintainer


  • person_outline Vince Buffalo

Scythe citations

 (55)
library_books

Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

2018
mSystems
PMCID: 5893860
PMID: 29657970
DOI: 10.1128/mSystems.00039-18

[…] degrees of diversity (; ). Metagenomic data sets were processed by using SolexaQA () with a maximum expected error of 1% and a minimum length of 50 bp, and adapter contamination was clipped by using Scythe (https://github.com/vsbuffalo/scythe). For paired-end samples, only the forward reads were used. Short Read Archive (SRA) identifiers are provided in for all of the data sets except Iowa conti […]

library_books

High density SNP mapping and QTL analysis for time of leaf budburst in Corylus avellana L.

2018
PLoS One
PMCID: 5880404
PMID: 29608620
DOI: 10.1371/journal.pone.0195408

[…] Raw reads were analyzed with Scythe (https://github.com/vsbuffalo/scythe) to filter out contaminant substrings and Sickle (https://github.com/najoshi/sickle) to remove reads with poor quality ends (Q<30). Illumina reads were de-m […]

call_split

Draft Genome Sequence of Lysinibacillus fusiformis Strain Juneja, a Laboratory Derived Pathogen of Drosophila melanogaster

2018
Genome Announc
PMCID: 5794956
PMID: 29437109
DOI: 10.1128/genomeA.01571-17
call_split See protocol

[…] system Nano run, yielding 761,837 paired-end 250-bp reads. We also used the MinION device (Oxford Nanopore Technologies, Oxford, UK) to obtain 3,251 long reads. Raw Illumina reads were filtered using Scythe (see https://github.com/vsbuffalo/scythe), and reads mapping to PhiX were discarded, yielding a total of 746,482 paired-end reads.We assembled the Lysinibacillus genome using Unicycler () with […]

call_split

Draft Genome Sequence of Pseudomonas putida CA 3, a Bacterium Capable of Styrene Degradation and Medium Chain Length Polyhydroxyalkanoate Synthesis

2018
Genome Announc
PMCID: 5786685
PMID: 29371359
DOI: 10.1128/genomeA.01534-17
call_split See protocol

[…] ing was performed by Macrogen (Seoul, South Korea) using Illumina’s MiSeq paired-end technology. The sequencing generated 3,332,054 reads and 1,002,948,254 bp. The raw data had adapters trimmed using Scythe v.0.994 (see https://github.com/vsbuffalo/scythe) and Sickle v.1.33 programs (). The reads were then quality filtered and trimmed using FaQCs v.1.35 for a minimum quality value (QV) score of >2 […]

library_books

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

2018
BMC Genomics
PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] on of the de novo transcriptome reconstruction and analysis pipeline is given in Fig. . The sequencing reads in fastq format were subjected to pre-processing where adapter sequences were removed with Scythe v0.9944 BETA [] and low quality reads were trimmed with Sickle v1.210 [] (Phred quality score > 30). Given that of the four species studied, a reference genome is currently only available for A […]

library_books

Phylogeny and putative virulence gene analysis of Bartonella bovis

2017
PMCID: 5938196
PMID: 29311425
DOI: 10.1292/jvms.17-0448

[…] ng Illumina platform with 100 bp paired-end reads. The reads were then subjected to adapters and low quality reads trimming based on Q25 using Trimmomatics [] and Sycthe (https://github.com/vsbuffalo/scythe). String Graph Assembler (SGA) [] was used for error correction. After pre-analysis, the reads were subjected to de novo genome assembly, using IDBA-UD, a de novo assembler for sequencing data […]

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