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BBMerge specifications


Unique identifier OMICS_17799
Name BBMerge
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Brian Bushnell

Additional information

BBMerge citations


Salmonella enterica Prophage Sequence Profiles Reflect Genome Diversity and Can Be Used for High Discrimination Subtyping

Front Microbiol
PMCID: 5945981
PMID: 29780368
DOI: 10.3389/fmicb.2018.00836

[…] m PHRED quality score of Q10 from the 3′ end using the BBDuk tool ( Trimmed reads shorter than 64 bases were discarded and the remainders were merged using BBMerge ( Both paired and unpaired reads were kept for de novo assembly, which was performed using SPAdes genome assembler 3.10.1 algorithm (Bankevich et al […]


Draft Genome Sequence of Raoultella ornithinolytica Strain HH3

Genome Announc
PMCID: 5897809
PMID: 29650579
DOI: 10.1128/genomeA.00270-18
call_split See protocol

[…] nc.) using the version 3 sequencing kit. A total of 1,491,678 paired-end reads (300 bp) were generated.Adapter sequences and low-quality bases were trimmed (bbduk), and overlapping pairs were merged (bbmerge) using the BBtools software suite ( Preprocessed reads were assembled using SPAdes version 3.10.1 () and polished with Pilon version 1.22 (). The as […]


Long Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field Experiment

Front Microbiol
PMCID: 5816784
PMID: 29487575
DOI: 10.3389/fmicb.2018.00144

[…] sorting. Reads with a final length <100 bp after adaptor clipping were discarded. Sequences were oriented into the forward and reverse primer direction. Forward and reverse reads were combined using BBMerge 34.48. Datasets of combined reads were analyzed in the SILVAngs analysis pipeline. Using the SILVA Incremental Aligner [SINA version 1.2.10 for ARB SVN (revision 21008)] () all sequence reads […]


Identifying genome wide immune gene variation underlying infectious disease in wildlife populations – a next generation sequencing approach in the gopher tortoise

BMC Genomics
PMCID: 5775545
PMID: 29351737
DOI: 10.1186/s12864-018-4452-0
call_split See protocol

[…] d used those previously identified variants for variant quality score filtering. Briefly, we performed adapter and quality trimming with TRIMMOMATIC v0.32 [], merged overlapping paired-end reads with BBMerge v5.4 (, aligned merged and unpaired reads and paired reads separately to the C. p. bellii 3.0.3 genome [] using BWA-MEM v0.7.12 [], then less stringentl […]


Infection via mosquito bite alters Zika virus tissue tropism and replication kinetics in rhesus macaques

Nat Commun
PMCID: 5727388
PMID: 29235456
DOI: 10.1038/s41467-017-02222-8
call_split See protocol

[…] files from the paired-read Illumina miSeq dataset were merged, trimmed, and normalized using the bbtools package ( and Seqtk ( was used to merge reads, and to trim primer sequences by setting the forcetrimleft parameter 22. All other parameters are set to default values. These reads were then mapped to the referenc […]


Global DNA Methylation Patterns Can Play a Role in Defining Terroir in Grapevine (Vitis vinifera cv. Shiraz)

Front Plant Sci
PMCID: 5670326
PMID: 29163587
DOI: 10.3389/fpls.2017.01860

[…] first demultiplexed using GBSX () and filtered to remove any reads that did not match the barcode sequence used for library construction. Following demultiplexing, paired-end reads were merged using bbmerge in bbtools package (). Merged reads were next aligned to the 12X grapevine reference genome. Alignment BAM files where then used to generate a read count matrix with marker sequence tags, and […]

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