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SeqCluster specifications

Information


Unique identifier OMICS_07768
Name SeqCluster
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input format FASTQ
Output data Count matrix
Biological technology Illumina
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Version 0.99.10
Stability Stable
Requirements
bcbio, pydebtools, pysam
Maintained Yes

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Documentation


Maintainer


  • person_outline Eulalia Martí

Publication for SeqCluster

SeqCluster citations

 (3)
library_books

Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

2018
PLoS One
PMCID: 5837101
PMID: 29505615
DOI: 10.1371/journal.pone.0193527

[…] Sequences fulfilling QC were used as the input for the seqBuster/seqCluster tool that retrieves three matrices of counts: i) miRNA, ii) isomiRs, and iii) small RNA clusters [, ]. In order to detect miRNAs and isomiRs, reads were mapped to hairpins released from miR […]

call_split

Cross Species Y Chromosome Function Between Malaria Vectors of the Anopheles gambiae Species Complex

2017
Genetics
PMCID: 5629335
PMID: 28860320
DOI: 10.1534/genetics.117.300221
call_split See protocol

[…] re, the sequence of each transcript was blasted against the A. gambiae PEST RepeatMasker library provided by Vectorbase.org. For the small RNA dataset. we generated a count matrix using Seqbuster and SeqCluster suites (). and used DESeq2 () for differential expression analysis and log2 transformation of the count data. Only putative small RNA loci with a mean expression of >5 counts across samples […]

library_books

Computational Prediction of miRNA Genes from Small RNA Sequencing Data

2015
Front Bioeng Biotechnol
PMCID: 4306309
PMID: 25674563
DOI: 10.3389/fbioe.2015.00007

[…] pping. In this case, it would seem reasonable to assume that the read should be mapped to the highly expressed rRNA locus. Some work has already been made toward overcoming these challenges. The tool SeqCluster first fuses reads that overlap in sequence in a tiled way, and subsequently maps the fused sequences to the genome (Pantano et al., ). These methods can resolve many, although not all, ambi […]

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