From: Genome-wide sequencing as a first-tier screening test for short tandem repeat expansions
Features | lobSTR | RepeatSeq | HipSTR | TRED | EH | STRetch | exSTRa | GangSTR |
---|---|---|---|---|---|---|---|---|
Outputs repeat length? | Y | Y | Y | Y | Y | Y | N | Y |
Sequencing reads | Single- and paired-end | Single- and paired-end | Single- and paired-end | Paired-end | Paired-end | Paired-end | Paired-end | Paired-end |
Sequencing platforms supported | Illumina, Sanger, 454, and IonTorrent | Illumina | Illumina | Illumina | Illumina | Illumina | Illumina | Illumina |
Library prep. supported | PCR and PCR-free | n.a. | PCR and PCR-free | PCR and PCR-free | PCR and PCR-free | PCR and PCR-free | PCR and PCR-free | PCR and PCR-free |
Library prep. (rcmd) | None | None | None | None | PCR-free | PCR-free | None | None |
Aligners (rcmd) | lobSTR and BWA-MEM | Novoalign and Bowtie 2 | Indel-sensitive aligner | None | None | None | Bowtie 2 | None |
Analysis approach | Targeted and GW | Targeted and GW | Targeted and GW | Targeted | Targeted | GW | Targeted and GW | Targeted and GW |
NGS data type supported | WGS | WGS | WGS | WGS | WGS and ES | WGS and ES | WGS and ES | WGS and ES |
NGS data format | .bam, .fastq, or .fasta | .bam | .bam | .bam | .bam or .cram | .bam or .fastq | .bam | .bam |
Built-in stutter correction modela | Y | Y | Y | Y | n.a. | n.a. | n.a. | Y |
Test of significance | N | N | N | N | N | Y | Y | N |
Read types used | Spanning | Spanning | Spanning | Spanning, flanking or partial, paired-end reads, and IRR | Spanning, flanking, and IRR/IRR pairs | Anchored IRR | Flanking and anchored IRR | Spanning, flanking, and IRR/IRR pairs |
Phasingb | n.a | n.a | Y | n.a | n.a | n.a | n.a | n.a |
PL | C++ | C++ | C++ | Python | C++ | Java | Perl and R | C++ |
Sizing limitation | RL | RL | RL | FL | Not limited | FL | n.a. | Not limited |
Control dataset | Not required | Not required | Not required | Not required | Not required | Required | Not required | Not required |
Complex repeats | n.a. | n.a. | n.a. | n.a. | Y | n.a. | n.a. | N |
Output files | .vcf and .allelotype.stats | .repeatseq, .calls, and .vcf | .vcf | .vcf and .json | .vcf, .json, and .log | .tsv | p-values, ECDF, and tsum plots | .vcf |
Customized regions file | Possible | Possible | Possible | Possible | Possible | Possible, but not rcmd | Possible | Possible |