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Scythe specifications


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
Maintained Yes




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  • person_outline Vince Buffalo

Scythe citations


Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

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 ( 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 […]


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

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

[…] Raw reads were analyzed with Scythe ( to filter out contaminant substrings and Sickle ( to remove reads with poor quality ends (Q<30). Illumina reads were de-m […]


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

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, and reads mapping to PhiX were discarded, yielding a total of 746,482 paired-end reads.We assembled the Lysinibacillus genome using Unicycler () with […]


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

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 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 […]


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

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 […]


Phylogeny and putative virulence gene analysis of Bartonella bovis

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 ( 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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