TGICL pipeline

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
  • sclust
  • tclust

Versioning


Add your version

Maintainer


This tool is not maintained anymore.

Publication for TIGR Gene Indices clustering tools

TGICL IN pipelines

 (50)
2018
PMCID: 5877693
PMID: 29533976
DOI: 10.3390/ijms19030832

[…] to remove these reads before downstream analysis [55]., after filtering, we obtained clean reads from raw data, then trinity [56] was applied to perform de novo assembly with clean reads. next, tgicl [57] was used to cluster transcripts to unigenes. the transcriptome datasets are available in the ncbi repository, (https://submit.ncbi.nlm.nih.gov/subs/sra/?from) accession no. for library […]

2017
PMCID: 5282827
PMID: 28143394
DOI: 10.1186/s12864-017-3515-y

[…] to prove our assembly quality. for both strategies, redundancy and over-representation were reduced after trinity assemble by finding similar sequences using tigr gene indices clustering program (tgicl) and cluster database at high identity with tolerance (cd-hit) with minimum 90 and 95% similarity cut off respectively [53, 54]. the transdecoder was then used to identify the possible coding […]

2017
PMCID: 5294638
PMID: 28169358
DOI: 10.1038/srep42165

[…] 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 […]

2017
PMCID: 5357126
PMID: 28337395
DOI: 10.3732/apps.1700001

[…] bases (quality value <20). remaining reads were assembled into 66,482 transcripts using trinity version 2.3.2 (grabherr et al., 2011), which were then clustered into 47,628 unigenes with tgicl version 2.1 (pertea et al., 2003)., using the microsatellite identification tool (misa) (thiel et al., 2003), microsatellite regions in the unigenes were screened according to the following […]

2017
PMCID: 5464669
PMID: 28594956
DOI: 10.1371/journal.pone.0179243

[…] raw-reads were considered as clean-reads. de novo assembly in each sample was conducted using trinity (version 20120608). then the unigenes derived from the trinity outputs were clustered by tgicl [46,47]. the consensus cluster sequences and singletons make up the unigenes dataset. the annotation of unigenes were performed via a ncbi blastx against non-redundant (nr) and swissprot […]

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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