| Rank . | Software . | Pros . | Cons . | Best Options . |
|---|---|---|---|---|
| 1= | NovoAlign IUPAC | – Large number of mapped reads – High alignment precision and low reference bias – Fast execution | – Requires variation information from target populations – Some options are proprietary– Requires a license to unlock multi-threading and additional functionality | NOV1 NOV2 |
| 1= | BWA aln | – Large number of mapped reads – High alignment precision and low bias | – Slow execution | BWA1 BWA2 |
| 3 | BWA mem | – Large number of mapped reads – High alignment precision and low bias – Fast execution | – Optimized for reads ≥70 bp | BWA8 |
| 4= | NovoAlign | – Large number of mapped reads – Fast execution | – Significant reference bias | NOV2 |
| 4= | Bowtie2 | – High precision if using stringent mapQ filter – Fast execution | – Significant data loss when using stringent mapQ filter – Additional bias in analyses when using stringent mapQ filter – Low sensitivity for contaminants | BWT3 BWT4 BWT5 |
| Rank . | Software . | Pros . | Cons . | Best Options . |
|---|---|---|---|---|
| 1= | NovoAlign IUPAC | – Large number of mapped reads – High alignment precision and low reference bias – Fast execution | – Requires variation information from target populations – Some options are proprietary– Requires a license to unlock multi-threading and additional functionality | NOV1 NOV2 |
| 1= | BWA aln | – Large number of mapped reads – High alignment precision and low bias | – Slow execution | BWA1 BWA2 |
| 3 | BWA mem | – Large number of mapped reads – High alignment precision and low bias – Fast execution | – Optimized for reads ≥70 bp | BWA8 |
| 4= | NovoAlign | – Large number of mapped reads – Fast execution | – Significant reference bias | NOV2 |
| 4= | Bowtie2 | – High precision if using stringent mapQ filter – Fast execution | – Significant data loss when using stringent mapQ filter – Additional bias in analyses when using stringent mapQ filter – Low sensitivity for contaminants | BWT3 BWT4 BWT5 |
| Rank . | Software . | Pros . | Cons . | Best Options . |
|---|---|---|---|---|
| 1= | NovoAlign IUPAC | – Large number of mapped reads – High alignment precision and low reference bias – Fast execution | – Requires variation information from target populations – Some options are proprietary– Requires a license to unlock multi-threading and additional functionality | NOV1 NOV2 |
| 1= | BWA aln | – Large number of mapped reads – High alignment precision and low bias | – Slow execution | BWA1 BWA2 |
| 3 | BWA mem | – Large number of mapped reads – High alignment precision and low bias – Fast execution | – Optimized for reads ≥70 bp | BWA8 |
| 4= | NovoAlign | – Large number of mapped reads – Fast execution | – Significant reference bias | NOV2 |
| 4= | Bowtie2 | – High precision if using stringent mapQ filter – Fast execution | – Significant data loss when using stringent mapQ filter – Additional bias in analyses when using stringent mapQ filter – Low sensitivity for contaminants | BWT3 BWT4 BWT5 |
| Rank . | Software . | Pros . | Cons . | Best Options . |
|---|---|---|---|---|
| 1= | NovoAlign IUPAC | – Large number of mapped reads – High alignment precision and low reference bias – Fast execution | – Requires variation information from target populations – Some options are proprietary– Requires a license to unlock multi-threading and additional functionality | NOV1 NOV2 |
| 1= | BWA aln | – Large number of mapped reads – High alignment precision and low bias | – Slow execution | BWA1 BWA2 |
| 3 | BWA mem | – Large number of mapped reads – High alignment precision and low bias – Fast execution | – Optimized for reads ≥70 bp | BWA8 |
| 4= | NovoAlign | – Large number of mapped reads – Fast execution | – Significant reference bias | NOV2 |
| 4= | Bowtie2 | – High precision if using stringent mapQ filter – Fast execution | – Significant data loss when using stringent mapQ filter – Additional bias in analyses when using stringent mapQ filter – Low sensitivity for contaminants | BWT3 BWT4 BWT5 |
This PDF is available to Subscribers Only
View Article Abstract & Purchase OptionsFor full access to this pdf, sign in to an existing account, or purchase an annual subscription.
