inGAP | Tool name | inGAP |
|---|
| URL | http://sourceforge.net/projects/ingap/ |
|---|
| Important features | 1. InGAP, which is guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms.
2. It can also help with completing genome assembly and comparative genome analysis.
3. InGAP can detect SNPs and indels by comparing sequence data generated by either Roche/454 and/or Illumina sequencing technologies, with a reference sequence, regardless read lengths and numbers. |
|---|
| Citations | Qi J, Zhao F, Buboltz A, Schuster SC. inGAP: an integrated next-generation genome analysis pipeline. Bioinformatics. 2010 Jan 1;26(1):127-9. Epub 2009 Oct
30. PubMed PMID: 19880367; PubMed Central PMCID: PMC2796817. |
|---|
| Year of publication | 2010 |
|---|
| Rank by usage frequency | 100 |
|---|
| Comments | |
|---|
| Function | Visualization, SNP discovery, Indel discovery |
|---|
| Category | Free, Downloadable |
|---|
| License | GNU GPL |
|---|
| Status | |
|---|
| Input file format | FATA, FASTQ |
|---|
| Output file format | |
|---|
| Operating system | Windows 32/64bit
Linux/Unix 32/64bit
Mac OS X 32/64bit |
|---|
| Operating language | JAVA |
|---|
| Platform | Sanger,
Roche 454, Illumina/Solexa |
|---|
| Maintained by | |
|---|
| Downloadable file format | |
|---|
| Submission file format | |
|---|
| |
