CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies

Bioinformatics
Hrant HovhannisyanToni Gabaldón

Abstract

Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing genetic material from divergent organisms. A crucial step in these studies is identifying from which organism each sequencing read originated, and the experimental design should be directed to minimize biases caused by cross-mapping of reads to incorrect source genomes. Additionally, pooling of sufficiently different genetic material into a single sequencing library could significantly reduce experimental costs but requires careful planning and assessment of the impact of cross-mapping. Having these applications in mind we designed Crossmapper, the first to our knowledge tool able to assess cross-mapping prior to sequencing, therefore allowing optimization of experimental design. Using any combination of reference genomes, Crossmapper performs read simulation and back-mapping of those reads to the pool of references, quantifies and reports the cross-mapping rates for each organism. Crossmapper performs these analyses with numerous user-specified parameters, including, among others, read length, read layout, coverage, ma...Continue Reading

References

May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Oct 30, 2012·Bioinformatics·Alexander DobinThomas R Gingeras
Oct 1, 2012·IEEE International Conference on Bioinformatics and Biomedicine Workshops·Shuai Yuan, Zhaohui Qin
Oct 4, 2015·Applied and Environmental Microbiology·Pedro González-TorresJosefa Antón
May 18, 2016·Nature Reviews. Genetics·Sara GoodwinW Richard McCombie
Feb 17, 2017·PLoS Pathogens·Alexander J WestermannJörg Vogel
Mar 25, 2017·Genome Biology and Evolution·Brian P H MetzgerJoseph D Coolon
May 4, 2017·PloS One·Thomas Nordahl PetersenThomas Sicheritz-Pontén
Sep 29, 2017·Current Opinion in Microbiology·Thomas WolfJörg Linde
Nov 21, 2017·Nucleic Acids Research·Daniel R ZerbinoPaul Flicek
Dec 9, 2017·Nature Biotechnology·Christopher QuinceNicola Segata
Feb 28, 2018·Methods in Molecular Biology·Alexander J Westermann, Jörg Vogel

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Methods Mentioned

BETA
exome sequencing

Software Mentioned

Ensembl
Crossmapper
DNA
- t
BWA
MEM
GitHub
STAR

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