2011 NGS Field Guide – Table 1 – Instrument Use Grades

Table 1a. Utility of 2nd and 3rd generation DNA sequencing platforms for de novo assemblies of different templates. Table assumes FLX+, MiSeq, Ion Torrent 318, and PacBio achieve stated goals (independent of stated time-lines). Initial letter indicates the author’s opinion of the overall utility (grade) for a platform for a specific application. Utility grades combine data characteristics (amount, quality, length), cost of data, and ease of assembling the data into the final desired product. Major considerations for utility grades are noted.

N.B. If you think that these data are inaccurate or out of date, please post a comment below and we’ll attempt to include it in our next update (currently scheduled for May 2012).

Platform – instrument Application: de novo assemblies
BACs, plastids & microbial genomes transcriptome plant & animal genome
454 – GS Jr. B – good but expensive C – need multiple runs, expensive D – cost prohibitive
454 – FLX+ A – good, need to multiplex to be economical A – good but expensive, not best for short RNAs B/C – good as part of a mixed platform strategy, expensive to use alone
Illumina – MiSeq B – good, assembly more challenging than 454 B – may need multiple runs, assembly more challenging than 454 C – expensive, use to validate libraries from HiSeq
Illumina – HiSeq B/C – more data than needed unless highly indexed; assembly more challenging than 454 A/B – good, assembly more challenging than 454 but much more data for analysis A – primary data type in many current projects; requires mate pair libraries
SOLiD – 5500 C – more data than needed unless highly indexed; assembly more challenging than 454 or Illumina C/D – short reads make assembly challenging or impossible C/D – short reads make assembly challenging or impossible
HeliScope D – read lengths make assemblies difficult to impossible F – read lengths are too short F – read lengths are too short
Ion Torrent – 314 C – OK, but reads are shorter than Illumina & as expensive as 454 C – OK, but reads are shorter than Illumina & as expensive as 454 D – cost prohibitive, reads shorter than alternatives
Ion Torrent – 318 B – good, data more challenging to assemble than 454 or Illumina B/C – good, data more challenging to assemble than 454 or Illumina C – high cost, data more challenging to assemble than 454 or Illumina
PacBio – RS B – requires high coverage due to high error rates B – expensive, short RNA will be challenging B/D – strobed reads could be good as part of mixed platform strategy; cost prohibitive to use alone





Table 1b. Utility of 2nd and 3rd generation DNA sequencing platforms for resequencing applications. Table assumes FLX+, MiSeq, Ion Torrent 318, and PacBio achieve stated goals (independent of stated time-lines). Initial letter indicates the author’s opinion of the overall utility (grade) for a platform for a specific application. Utility grades combine data characteristics (amount, quality, length), cost of data, and ease of assembling the data into the final desired product. Major considerations for utility grades are noted.

Platform – instrument Application: resequencing
targeted loci transcript counting genome resequencing
454 – GS Jr. B – good but expensive, need to limit loci D – cost prohibitive D – cost prohibitive for large genomes
454 – FLX+ B – good but expensive, should limit loci D – cost prohibitive for large genomes C/D – cost prohibitive for large genomes
Illumina – MiSeq A/B – good, fewer and higher cost reads than Hi Seq B – more expensive than HiSeq or SOLiD C – expensive for large genomes
Illumina – HiSeq A – primary data type in many current projects; best for many loci A – primary data type in many current projects A – primary data type in many current projects
SOLiD – 5500 A/B – good for many loci and many indexed samples A – primary data type in many current projects A – primary data type in many current projects
HeliScope C – difficult to assemble loci A/B – best single-molecule platform; less available platform, shortest max read length (limits mapping) B – read lengths shorter than alternatives
Ion Torrent – 314 C – OK but expensive, need to limit loci D – cost prohibitive D – cost prohibitive
Ion Torrent – 318 B – good, slightly less data per run than MiSeq B – more expensive than HiSeq or SOLiD C – expensive for large genomes
PacBio – RS D – requires high coverage due to high error rates D – cost prohibitive D – cost prohibitive for large genomes





Table 1c. Utility of 2nd and 3rd generation DNA sequencing platforms for various applications. Table assumes FLX+, MiSeq, Ion Torrent 318, and PacBio achieve stated goals (independent of stated time-lines). Initial letter indicates the author’s opinion of the overall utility (grade) for a platform for a specific application. Utility grades combine data characteristics (amount, quality, length), cost of data, and ease of assembling the data into the final desired product. Major considerations for utility grades are noted.

Platform – instrument Various Applications
metagenomics1 mutation detection2 other limitations
454 – GS Jr. A/B – good, but costs limit sample number and depth D – cost prohibitive will the GS Jr. be upgradable to longer read lengths?
454 – FLX+ A – good, long reads maximise data per read C – expensive, good for identifying clusters will 454 run costs come down?
Illumina – MiSeq B/C – OK, limited by short reads, bases in phase* B – more expensive than HiSeq or SOLiD will the MiSeq platform perform as advertised?
Illumina – HiSeq B – OK, limited by short reads, bases in phase* A – primary data type in many current projects will Illumina settle on a data format?
SOLiD – 5500 D – limited by short reads A – primary data type in many current projects will read lengths increase?
HeliScope F – limited by short reads A/B – best single-molecule platform; less available platform will the company survive?
Ion Torrent – 314 C – limited by short reads and cost D – cost prohibitive will the price for this chip decrease?
Ion Torrent – 318 B – less read-length than alternatives; no phase issues B – more expensive than HiSeq or SOLiD when will this be available at advertised specifications?
PacBio – RS D – cost & insufficient accuracy except for short consensus sequence reads D – cost prohibitive & insufficient accuracy except for short consensus sequence reads when will new applications be available?



1Metagenomics – characterization of 16S sequences within and among microbial communities, primarily via sequencing amplicons.

2Mutation Detection – identification of rare sequence variants

*Most Illumina instruments require mixed base signals across reads, thus amplicon sequencing requires strategies to offset or randomize the beginning base of amplicons