Biobambam: Tools for read pair collation based algorithms on BAM files

Source Code for Biology and Medicine

Volumn 9, Issue 1, 2014, Pages

  Tischler, German ^a   Leonard, Steven ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Collation by read name; Duplicate marking; File format conversion; High throughput sequencing

Indexed keywords

EID: 84902705625     PISSN: None     EISSN: 17510473     Source Type: Journal    
DOI: 10.1186/1751-0473-9-13     Document Type: Review

References (36)

1. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. [http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract], 10.1093/bioinformatics/btp352, 2723002, 19505943.
2. The SAM file specification. [http://samtools.sourceforge.net/SAM1.pdf].
3. Ning Z, Cox AJ, Mullikin JC. SSAHA: a fast search method for large DNA databases. Genome Res 2001, 11(10):1725-1729. 10.1101/gr.194201, 311141, 11591649.
4. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324, 2705234, 19451168.
5. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010, 26(5):589-595. 10.1093/bioinformatics/btp698, 2828108, 20080505.
6. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
7. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012, 9(4):357-359. 10.1038/nmeth.1923, 3322381, 22388286.
8. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24(5):713-714. 10.1093/bioinformatics/btn025, 18227114.
9. Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967. 10.1093/bioinformatics/btp336, 19497933.
10. SMALT. [http://www.sanger.ac.uk/resources/software/smalt/].
11. Li H. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics 2012, 28(14):1838-1844. 10.1093/bioinformatics/bts280, 3389770, 22569178.
12. Picard. [http://picard.sourceforge.net/].
13. bamUtil. [http://genome.sph.umich.edu/wiki/BamUtil].
14. biobambam. [https://github.com/gt1/biobambam].
15. libmaus. [https://github.com/gt1/libmaus].
16. Döring A, Weese D, Rausch T, Reinert K. SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics 2008, 9:1-9. [http://dx.doi.org/10.1186/1471-2105-9-11], 10.1186/1471-2105-9-1, 2265676, 18173834.
17. Ramirez-Gonzalez R, Bonnal R, Caccamo M, MacLean D. Bio-samtools: ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. Source Code Biol Med 2012, 7(6). [http://www.scfbm.org/content/7/1/6].
18. Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E. Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res 2011, 21(5):734-740. [http://genome.cshlp.org/content/21/5/734.abstract], 10.1101/gr.114819.110, 3083090, 21245279.
19. io_lib in the Staden package. [http://sourceforge.net/projects/staden/files/io_lib/].
20. The Staden package. [http://staden.sourceforge.net/].
21. Bonfield JK, Whitwham A. Gap5-editing the billion fragment sequence assembly. Bioinformatics 2010, 26(14):1699-1703. [http://bioinformatics.oxfordjournals.org/content/26/14/1699.abstract], 10.1093/bioinformatics/btq268, 2894512, 20513662.
22. [EMBL:ERP001231]. [http://www.ebi.ac.uk/ena/data/view/ERP001231].
23. Genome Reference Consortium, human reference assembly release version 37. [ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/].
24. bam2fastq. [http://gsl.hudsonalpha.org/information/software/bam2fastq].
25. bampe2fqworphans. [http://seqanswers.com/forums/showpost.php?p=108412&postcount=26].
26. HG03520. [ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG03520/alignment/HG03520.chrom11.ILLUMINA.bwa.ESN.low_coverage.20130502.bam].
27. 1000 Genomes Project C. A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. 10.1038/nature09534, 3042601, 20981092.
28. HG00096. [ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/HG00096/alignment/HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20120522.bam].
29. [EMBL:SRP017681]. [http://www.ebi.ac.uk/ena/data/view/SRP017681].
30. Reference genome of Escherichia coli str. K-12 substr MG1655. [ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Escherichia_coli_K_12_substr__MG1655_uid57779/NC_000913.fna].
31. [EMBL:ERR239642]. [http://www.ebi.ac.uk/ena/data/view/ERR239642].
32. [EMBL:ERR217514]. [http://www.ebi.ac.uk/ena/data/view/ERR217514].
33. [EMBL:ERR196957]. [http://www.ebi.ac.uk/ena/data/view/ERR196957].
34. [EMBL:ERR328876]. [http://www.ebi.ac.uk/ena/data/view/ERR328876].
35. [EMBL:ERR054938]. [http://www.ebi.ac.uk/ena/data/view/ERR054938].
36. [EMBL:ERR328190]. [http://www.ebi.ac.uk/ena/data/view/ERR328190].