TGICL specifications

Information


Unique identifier OMICS_15143
Name TIGR Gene Indices clustering tools
Alternative name 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
Source code URL ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/
Maintained No

Subtools


  • mgblast
  • tclust
  • sclust

Versioning


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Documentation


Maintainer


This tool is not maintained anymore.

TGICL article

TGICL citations

 (11)
2017
PMCID: 5694954

[…] the reads using in-house script by theragen etex bio institute, republic of korea (table 2). trinity version 2.1.1 [6] was used to assemble the reads de novo [7] with default configuration while tigr gene indices clustering tools version 2.1 (identity; 0.94) [8] was used to omit redundant sequences and cluster them into non-redundant unigenes set. a total of 101,384 unigenes were found […]

2017
PMCID: 5294638

[…] the contigs and obtained sequences that cannot be extended on either end, which were defined as unigenes. finally, we assembled all the unigenes to form a single set of non-redundant unigenes using tgicl68. after clustering, the unigenes were divided into two classes: clusters and singletons. after assembly, blastx alignment was performed between unigenes and the protein databases […]

2015
PMCID: 4691031

[…] the adapters and low quality tags were removed, high-quality clean reads were obtained and assembled using trinity (trinityrnaseq_r2012-10-05) [55]. subsequently, unigenes were acquired using the tigr gene indices clustering tools (http://www.tigr.org/tdb/tgi.shtml) [56]. furthermore, the unigenes were annotated using the blastx algorithm against swiss-prot, trembl, ncbi, cdd, pfam and kog […]

2015
PMCID: 4604318

[…] were generated and these unigenes could not be extended on either end as assembled by trinity. a library named unigene-all was clustered among the four transcriptome libraries using an application tgicl to obtain non-redundant unigenes as long as possible (pertea et al., 2003). functional annotation of the unigenes was accomplished using blastx alignment (e < 0.00001) between the unigenes […]

2015
PMCID: 4502468

[…] gene index established by schafleitner et al. [27], 56,516 developed by wang et al. and 58,681 generated in house [2, 51]. these ests were assembled using the tigr gene indices clustering tools (tgicl) [29], and 87,492 potential unique ests were generated. a total of 71,999 in situ synthesized 60-mer oligonucleotide probes representing 39,724 sweetpotato genes were constructed […]

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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