TGICL statistics

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Citations per year

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

This map represents all the scientific publications referring to TGICL per scientific context
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Protocols

TGICL specifications

Information


Unique identifier OMICS_15143
Name TGICL
Alternative names TIGR Gene Indices clustering tools, NGICL
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data A multi-FASTA file.
Output data One or more ACE files containing CAP3 assemblies, a list of singletons.
Operating system Unix/Linux
Programming languages C, C++, Perl
Computer skills Advanced
Stability Stable
Requirements
glibc, libstdc++, cap3
Maintained No

Subtools


  • mgblast
  • tclust

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publication for TIGR Gene Indices clustering tools

TGICL citations

 (486)
library_books

Transcriptome and Co Expression Network Analyses Identify Key Genes Regulating Nitrogen Use Efficiency in Brassica juncea L.

2018
Sci Rep
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] D-HIT-EST version 4.6, a clustering program was used to search similar sequences with minimum similarity cut-off of 90% (http://weizhongli-lab.org/cd-hit). Another clustering step was performed using TGICL-CAP3 version 2.2.26 program at 90% identity to cluster the similar sequences (http://www.tigr.org/tdb/tgi/software). […]

call_split

Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

2018
BMC Plant Biol
PMCID: 5941469
PMID: 29739322
DOI: 10.1186/s12870-018-1296-3
call_split See protocol

[…] y (version: v2.0.6) [] was used to perform de novo assembly with clean reads from all 12 libraries with min_contig_length set to 150 and min_kmer_cov set to 3 and all other parameters set to default. Tgicl (version: v2.0.6) [] was used to cluster transcripts to Unigenes with repeat_stringency, minmatch, and minscore set to 0.95, 35, and 35, respectively, and all other parameters set to default. We […]

call_split

Byssus Structure and Protein Composition in the Highly Invasive Fouling Mussel Limnoperna fortunei

2018
Front Physiol
PMCID: 5911496
PMID: 29713291
DOI: 10.3389/fphys.2018.00418
call_split See protocol

[…] tions and sequenced on the Illumina Sequencing Platform HiSeqTM 2500 (Illumina, San Diego, CA, USA). The sequenced results were spliced by TRINITY software (Grabherr et al., ) with paired-end method. TGICL software was used to remove redundancy and get a set of final unigene as reference sequences. Raw data of L. fortunei foot transcriptome has been deposited into Sequence Read Archive (SRA) in NC […]

call_split

Development of novel EST SSR markers for ploidy identification based on de novo transcriptome assembly for Misgurnus anguillicaudatus

2018
PLoS One
PMCID: 5896994
PMID: 29649332
DOI: 10.1371/journal.pone.0195829
call_split See protocol

[…] [] to remove adaptor contamination, unqualified reads and sequences. High quality clean reads were pooled and de novo assembled using Trinity [] with default parameters, forming transcripts. Then the TIGR Gene Indices clustering tools (TGICL) (ver 2.1) [] were used to cluster and remove redundant transcripts, and identify unigenes (i.e., non-redundant transcripts), which were used for subsequent a […]

library_books

De novo assembly and analysis of the Artemisia argyi transcriptome and identification of genes involved in terpenoid biosynthesis

2018
Sci Rep
PMCID: 5895812
PMID: 29643397
DOI: 10.1038/s41598-018-24201-9

[…] forms were generated by splicing transcripts corresponding to paralogous genes. All such sequences were known as transcripts. Transcript analysis was performed to cluster and remove redundancies with TGICL (version 2.06, parameters: -l 30 -v 35) to acquire non-redundant sequences, termed unigenes. All unigenes were segmented into two categories: clusters (prefixed with CL) and singletons (prefixed […]

call_split

Response analysis of host Spodoptera exigua larvae to infection by Heliothis virescens ascovirus 3h (HvAV 3h) via transcriptome

2018
Sci Rep
PMCID: 5876357
PMID: 29599494
DOI: 10.1038/s41598-018-23715-6
call_split See protocol

[…] reads with low quality, reads containing adapters, or reads with unknown nucleotides >5%. The clean reads were de novo assembled by Trinity (version v2.0.6), followed by clustering to redundancy with Tgicl (version v2.0.6) to obtain unigenes. Blast (http://blast.ncbi.nlm.nih.gov/Blast.cgi) was used to annotate NT, NR (ftp://ftp.ncbi.nlm.nih.gov/blast/db), COG (http://www.ncbi.nlm.nih.gov/COG), KEG […]


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TGICL institution(s)
The Institute for Genomic Research, Chinakville, MD, USA; Department of Computer Science, Iowa State University, Ames, IA, USA

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