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FRAMA specifications

Information


Unique identifier OMICS_11024
Name FRAMA
Alternative name from RNA-seq to annotated mRNA assembly
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A reference transcriptome and RNA-seq data.
Input format GenBank, FASTQ
Output data A representative compilation of transcripts, a so-called transcript catalog, with CDSs and mRNA boundaries annotated.
Operating system Unix/Linux
Programming languages Perl, R
Computer skills Advanced
Version 20151019
Stability Stable
Requirements
Trinity, samtools, bamtools, bowtie/bowtie2, EMBOSS, MAFFT, GENSCAN, RepeatMasker, CD-HIT-EST, TGICL, WU-BLAST, NCBI-BLAST, GenblastA, Perl::BioPerl, Parallel::ForkManager, Set::IntSpan, FileHandle::Unget, R::plyr, ggplot, reshape, gridExtra, annotate, GO.db, KEGG.db
Maintained Yes

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Versioning


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Documentation


Maintainers


  • person_outline Martin Bens
  • person_outline Karol Szafranski

Publication for from RNA-seq to annotated mRNA assembly

FRAMA citations

 (3)
call_split

Long lived rodents reveal signatures of positive selection in genes associated with lifespan

2018
PLoS Genet
PMCID: 5884551
PMID: 29570707
DOI: 10.1371/journal.pgen.1007272
call_split See protocol

[…] ly published de novo transcriptome assembly []. RNA-seq data for six mole-rat species was obtained from GenBank Sequence Read Archive, study SRP061925 []. The reads were assembled and annotated using FRAMA as described in [].For Ansell’s and giant mole-rat, purification of RNA from 13 and 17 tissues, respectively, was done using Qiagen RNeasy Mini Kit following the manufacturer's description. Nove […]

call_split

The HACMS program: using formal methods to eliminate exploitable bugs

2017
Philos Trans A Math Phys Eng Sci
PMCID: 5597724
PMID: 28871050
DOI: 10.1098/rsta.2015.0401
call_split See protocol

[…] Now, the situation has improved: many robust formal-methods tools are publicly available with suitable documentation and licences. Examples include ACL2, Alt-Ergo, Astree, Bedrock, Boogie, Coq, CVC4, Frama-C, Isabell, KLEE, PVS, SLAM, TLA+, VCC, Yices2, Z3 and many others. These tools are sufficiently developed that they can be productively used by people other than the original developers.A fourt […]

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Parallel evolution of genes controlling mitonuclear balance in short‐lived annual fishes

2017
Aging Cell
PMCID: 5418189
PMID: 28295945
DOI: 10.1111/acel.12577

[…] cies (N. furzeri, N. kadleci, N. kuhntae, N. pienaari, N. rachovii, and N. korthausae) and A. striatum from transcriptome catalogs that were recently assembled and annotated (Reichwald et al., ) with FRAMA (Bens et al., ). The reads were adapter clipped with seqprep (https://github.com/jstjohn/SeqPrep) and quality trimmed with sickle (Joshi & Fass, ) before assembly [for more information about tis […]

Citations

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FRAMA institution(s)
Leibniz Institute on Ageing - Fritz Lipmann Institute, Jena, Germany; Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
FRAMA funding source(s)
Supported by the Bundesministerium für Bildung und Forschung (BMBF) and the Leibniz-Gesellschaft through the Senatsausschusswettbewerb (SAW), grant SAW-2012-FLI-2, as well as the Deutsche Forschungsgemeinschaft (DFG), grant PL 173/8-1.

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