Genomics tools¶

Quality control¶

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

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

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

References

[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: http://www.nature.com.gate1.inist.fr/nmeth/journal/v12/n1/full/nmeth.3176.html, 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: http://www.biomedcentral.com/1471-2105/10/421/abstract, 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: http://www.gigasciencejournal.com/content/4/1/39/abstract, 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: http://arxiv.org/abs/1303.3997.

[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: http://bioinformatics.oxfordjournals.org/content/26/5/589, 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.