Genomics tools

Quality control


Name Version Galaxy wrapper
CD-HIT [5][11] 4.6.4 cdhit
Format CD-HIT output   format_cd_hit_output

Sorting and Prediction

Name Version Galaxy wrapper
SortMeRNA [6] 2.1b sortmerna
FragGeneScan [12] 1.30 fraggenescan

Similarity search and alignment

Name Version Galaxy wrapper
NCBI BLAST [2][3] 2.2.30 ncbi_blast_plus
Diamond [1] 0.8.24 diamond
HMMER3 [4] 3.1b2 hmmer3


Name Version Galaxy wrapper
BWA [9][10][8] 0.7.12 bwa
Bowtie2 [7] 2.3.2 bowtie2


[1]Benjamin Buchfink, Chao Xie, and Daniel H. Huson. Fast and sensitive protein alignment using DIAMOND. Nat Meth, 12(1):59–60, January 2015. URL:, doi:10.1038/nmeth.3176.
[2]Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, and Thomas L. Madden. BLAST+: architecture and applications. BMC Bioinformatics, 10(1):421, December 2009. URL:, doi:10.1186/1471-2105-10-421.
[3]Peter JA Cock, John M. Chilton, Björn Grüning, James E. Johnson, and Nicola Soranzo. NCBI BLAST+ integrated into Galaxy. GigaScience, 4(1):39, August 2015. URL:, doi:10.1186/s13742-015-0080-7.
[4]Robert D Finn, Jody Clements, and Sean R Eddy. Hmmer web server: interactive sequence similarity searching. Nucleic acids research, 39(suppl_2):W29–W37, 2011.
[5]Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu, and Weizhong Li. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics, 28(23):3150–3152, December 2012. doi:10.1093/bioinformatics/bts565.
[6]Evguenia Kopylova, Laurent Noé, and Hélène Touzet. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics, 28(24):3211–3217, December 2012. doi:10.1093/bioinformatics/bts611.
[7]Ben Langmead and Steven L Salzberg. Fast gapped-read alignment with bowtie 2. Nature methods, 9(4):357–359, 2012.
[8]Heng Li. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997 [q-bio], March 2013. arXiv: 1303.3997. URL:
[9]Heng Li and Richard Durbin. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14):1754–1760, July 2009. doi:10.1093/bioinformatics/btp324.
[10]Heng Li and Richard Durbin. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics, 26(5):589–595, March 2010. URL:, doi:10.1093/bioinformatics/btp698.
[11]Weizhong Li and Adam Godzik. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13):1658–1659, July 2006. doi:10.1093/bioinformatics/btl158.
[12]Mina Rho, Haixu Tang, and Yuzhen Ye. Fraggenescan: predicting genes in short and error-prone reads. Nucleic acids research, 38(20):e191–e191, 2010.