BAM2fastx statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BAM2fastx

Tool usage distribution map

This map represents all the scientific publications referring to BAM2fastx per scientific context
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BAM2fastx specifications


Unique identifier OMICS_31938
Name BAM2fastx
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format BAM
Output format FASTA,FASTQ
Biological technology Pacific Biosciences
Operating system Unix/Linux
Programming languages C++, Java, Perl, Python, Shell (Bash), Other
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.3.0
Stability Stable
Maintained Yes




No version available

BAM2fastx citations


A massively parallel strategy for STR marker development, capture, and genotyping

Nucleic Acids Res
PMCID: 5587753
PMID: 28666376
DOI: 10.1093/nar/gkx574

[…] calling workflow for WGS described at, followed by filtering to only keep putative STR variants. We converted the downloaded BAM alignments to raw FASTQ sequences using bam2fastx script supplied with TopHat (), and then used lobSTR () to identify, align, and genotype all putative heterozygous STRs in the individual using the lobSTR index for hg19. We were able to gen […]


Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells

BMC Genomics
PMCID: 4301880
PMID: 25418962
DOI: 10.1186/1471-2164-15-1016

[…] uencers were processed using the exome analysis pipeline (Amelieff). The pipeline performed the following steps. Some sequence data were provided in BAM format and were converted to fastq format with bam2fastx (tophat-2.0.4) [] for use in the pipeline. First, raw sequence data were cleaned up with QCleaner software (Amelieff): low-quality reads (>20% of the base calls with a Phred score <20) were […]


Capture and Amplification by Tailing and Switching (CATS)

RNA Biol
PMCID: 4179956
PMID: 24922482
DOI: 10.4161/rna.29304
call_split See protocol

[…] itive alignment mode. Short reads not corresponding to cel-mir-39 were selected using Samtools (version 0.1.19) and converted from SAM format to FASTQ for downstream alignment compatibility using the bam2fastx script included in TopHat2 (version 2.0.10)., The 1000 Genomes Project reference genome (GRCh37 with decoy 5) was used for alignment of short reads to the human genome. Bowtie2 with local al […]

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