| Software | Version | Input | Output | Location(machine/folder)
|
| Newbler | 2.3(091027_1459) | | | panflam,panpyro
|
| Phrap | 0.990329(Phrap0.990329_patch) | | | panflam
|
| Phrap | 1.090518 | | | panflam
|
| Consed | 090206 | | | panflam
|
| CABOG(celera) | 6.1 | sanger, 454(.sff), illumina(fastq), fastq | CABOG_output | panflam,panpyro
|
| maq | 0.7.1 | ref:fasta, read:illumina, long read(not good) | | panflam,panpyro
|
| abyss [[1]] | 1.2.0 | 454, illumina | | panflam
|
| SOAPdenovo | 1.04 | illumina | | panflam
|
| SOAPaligner | | illumina | | panflam
|
| Corrector(soap package) | 1.00 | fasta,fastq | | panflam
|
| GapCloser(soap package) | 1.10 | fasta,fastq | | panflam
|
| MIRA | | sanger,454,illumina | |
|
| gapResolution | | newbler results | fasta,qual |
|
| Dupfinisher | | ace file | |
|
| AutoEditor | 1.20 | .contig(TIGR) | |
|
| rnammer | 1.2 | fasta | gff2 | panflam
|
| hmmer | 2.3.2(for rnammer), 3 | | | panflam.panpyro
|
| tRNAscan-SE | 1.23 | | | panflam,panpyro
|
| BlastViewer | | | | panflam
|
| M-GCAT | | | | panflam,panpyro
|
| bowtie | | illumina | |
|
| Velvet | | illumina | |
|
| MAQ | | illumina | |
|
| Polisher | | illumina | |
|
