Review Article
SNP Discovery through Next-Generation Sequencing and Its Applications
Table 1
List of most cited/used software for sequence assembly of NGS data. Source locations for these software are compiled in Table
4.
| | Name (current version) | Assembly type | Supported parameters | Output format | Platform | | (algorithm) | Color space | Read length | Gapped alignment | Paired-end |
| | CLC-Bio1 | Reference2 | Yes | Arbitrary | Yes | Yes | CLC-Bio | Linux/Windows/Mac OS X | | SeqMan NGen1 | Reference2 | Yes | Arbitrary | Yes | Yes | ACE, BAM | Windows/Mac OS X | | NextGENe1 | Reference2 | Yes | Arbitrary | Yes | Yes | Next
GENe | Windows/Mac OS X | | Bowtie (2) | Reference (FM-index) | Yes | Arbitrary | Yes | Yes | SAM | Linux/Windows/Mac OS X | | BWA | Reference (FM-index) | Yes | Arbitrary | Yes | Yes | SAM | Linux | | SOAP (3) | Reference (FM-index) | Yes | Arbitrary | No | Yes | SOAP2/3 | Linux | | MAQ (0.6.6) | Reference (Hashing reads) | Yes | ≤127 | Yes | Yes | MAQ | Linux/Solaris/Mac OS X | | Novoalign (2.07.07) | Reference
(Hashing reference) | Yes | Arbitrary | Yes | Yes | SAM | Linux/Mac OS X | | Mosaik (1.1.0018) | Reference
(Hashing reference) | Yes | Arbitrary | Yes | Yes | SAM | Linux/Windows/Mac OS X/Solaris | | SHRiMP (2.2.2) | Reference
(Hashing reference) | Yes | Arbitrary | Yes | Yes | SAM | Linux/Mac OS X | | Mira (3.4) | Reference2 | Yes | Arbitrary | Yes | Yes | FASTA, ACE | Linux |
|
|
Commercial software. 2Option for de novo assembly and modules included for variant calling.
|
