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fqtrim specifications


Unique identifier OMICS_28048
Name fqtrim
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Some read sequence data.
Input format FASTA,FASTQ
Operating system Unix/Linux
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Geo Pertea

fqtrim citations


Gene level differential analysis at transcript level resolution

Genome Biol
PMCID: 5896116
PMID: 29650040
DOI: 10.1186/s13059-018-1419-z

[…] elial cells. Five replicates for each condition were performed by the original experimenters, resulting in a total of ten single-end RNA-seq samples []. Reads were trimmed to remove poly-A tails with fqtrim-0.9.5 using the default parameters []. As discussed above in the “” section under “,” TCCs were obtained with the kallisto pseudo option, differential expression of TCCs was performed in sleuth […]


Pharmacologic Reprogramming Designed to Induce a Warburg Effect in Porcine Fetal Fibroblasts Alters Gene Expression and Quantities of Metabolites from Conditioned Media Without Increased Cell Proliferation

PMCID: 5804098
PMID: 29412741
DOI: 10.1089/cell.2017.0040

[…] m as single-end reads with read depth of 50 million reads/sample. The raw sequences (FASTQ) were subjected to quality check by FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/). The program fqtrim (https://ccb.jhu.edu/software/fqtrim/) was used to remove adapters, perform quality trimming (phred score >30) by sliding window scan (6 nucleotides), and select read length 30 nucleotides or l […]


Systemic HIV 1 infection produces a unique glial footprint in humanized mouse brains

PMCID: 5769612
PMID: 29084769
DOI: 10.1242/dmm.031773
call_split See protocol

[…] was analyzed, samples were deep sequenced using 100 bp/read, ≤40 million reads/sample using an Illumina HiSeq 2500 Sequence Analyzer (Illumina, Inc., San Diego, CA, USA). Reads were trimmed using the fqtrim (ccb.jhu.edu/software/fqtrim/) software to remove ambiguous bases from the reads. Read alignment and differential gene expression was performed using the programs from the Tuxedo RNA-seq tool p […]


Genome wide open chromatin regions and their effects on the regulation of silk protein genes in Bombyx mori

Sci Rep
PMCID: 5635003
PMID: 29018289
DOI: 10.1038/s41598-017-13186-6
call_split See protocol

[…] aligned reads were obtained.RNA-seq data were analyzed using standard methods,46]. The quality of the raw and processed reads was evaluated using FastQC (Version 0.11.1). PolyA tails were filtered by fqtrim (Version 0.93), and reads were aligned to the silkworm tRNA and rRNA database (http://www.silkdb.org/silkdb/doc/download.htm) using bowtie2 software (Version 2.2.9). Low-quality reads were remo […]


Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus

Genome Biol Evol
PMCID: 5604253
PMID: 28922871
DOI: 10.1093/gbe/evx157

[…] was constructed with an average insert size of 200 bp. All libraries were sequenced on an Illumina HiSeq 2000 platform. Prior to assembly, quality filtering and adaptor trimming were performed using Fqtrim software (version 0.9.4, http://ccb.jhu.edu/software/fqtrim/) and Prinseq (version 0.20.4) (). After preprocessing, reads shorter than 70 bp and those containing more than 5% ambiguous bases (N […]


Draft Genome Sequence of Mycobacterium avium 11

Genome Announc
PMCID: 5552987
PMID: 28798178
DOI: 10.1128/genomeA.00766-17

[…] g an Illumina MiSeq platform, generating a total of 8,879,671 paired-end reads (AITbiotech, Singapore). These paired-end reads were quality checked using FastQC and subsequently quality trimmed using fqtrim (https://ccb.jhu.edu/software/fqtrim) with a window size of 7, a minimum average Q score of 28, and a minimum posttrim length of 35. The resulting 8,386,266 paired-end reads after trimming were […]


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