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Cdbfasta specifications

Information


Unique identifier OMICS_19793
Name Cdbfasta
Alternative name Fasta file indexing and retrival tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA, FA
Output format FAI
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Geo Pertea <>

Cdbfasta in pipelines

 (2)
2017
PMCID: 5491103
PMID: 28662089
DOI: 10.1371/journal.pone.0179971

[…] low quality bases and remove short sequences (minimum length 150 bp; trim 3’ bases below q20; minimum mean quality q25; no ns). pairs where both reads passed quality control were extracted using a cdbfasta pipeline [] and converted to fasta format. the scaffolds generated by both assemblers were concatenated in geneious v7.0.5 [] using the parameters: no gaps allowed, minimum overlap 150, […]

2015
PMCID: 4570228
PMID: 26369560
DOI: 10.1186/s12870-015-0599-x

[…] comparisons using both replicates for branch and stem secondary xylem and a cutoff of false discovery rate (fdr) < =0.05. subsequently, differentially expressed unigenes were exported with the “cdbfasta” tool (http://compbio.dfci.harvard.edu/) with the contig name from assemblies of trinity database in .fasta format. the differentially expressed unigenes were annotated using blast2go []. […]


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Cdbfasta in publications

 (7)
PMCID: 5491103
PMID: 28662089
DOI: 10.1371/journal.pone.0179971

[…] low quality bases and remove short sequences (minimum length 150 bp; trim 3’ bases below q20; minimum mean quality q25; no ns). pairs where both reads passed quality control were extracted using a cdbfasta pipeline [] and converted to fasta format. the scaffolds generated by both assemblers were concatenated in geneious v7.0.5 [] using the parameters: no gaps allowed, minimum overlap 150, […]

PMCID: 5283065
PMID: 28140388
DOI: 10.1038/sdata.2016.131

[…] used to parse the taxonomic group information from the ncbi taxonomy database. transcripts with a top blast hit to viridiplantae (‘green plants’) were retained. the fasta files were filtered using cdbfasta (https://sourceforge.net/projects/cdbfasta/) providing the id of the transcripts to be retained. the busco scores were calculated for the filtered transcript sets to ensure that the assembly […]

PMCID: 4834321
PMID: 27110349
DOI: 10.1002/ece3.2041

[…] able s1) to conduct tblastn searches (e‐value cutoff = 1e‐10) against the zokor genome (over 100x of sequencing depth, unpublished). for each tas2r gene, the best‐hit scaffold was extracted using the cdbfasta program (lee et al. ) was then aligned with the corresponding mouse gene. the primers for amplification were designed according to the flanking sequence of the zokor scaffold using primer pre […]

PMCID: 4707443
PMID: 26793200
DOI: 10.3389/fpls.2015.01195

[…] (significance value < 0.05) in at least one comparison. in the absence of replicates, we used deseq’s blind method for dispersion estimates: fdr correction was disabled and padj reported as “1”. cdbfasta was used to retrieve specific fasta sequences from the assembled unigenes file. for hierarchical clustering (hcl; ), normalized read counts for each deg were retrieved from deseq; hcl […]

PMCID: 4570228
PMID: 26369560
DOI: 10.1186/s12870-015-0599-x

[…] comparisons using both replicates for branch and stem secondary xylem and a cutoff of false discovery rate (fdr) < =0.05. subsequently, differentially expressed unigenes were exported with the “cdbfasta” tool (http://compbio.dfci.harvard.edu/) with the contig name from assemblies of trinity database in .fasta format. the differentially expressed unigenes were annotated using blast2go []. […]


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