Table 1 Required external software packages
From: sciReptor: analysis of single-cell level immunoglobulin repertoires
Software | Version | Additional packages/comments |
|---|---|---|
IgBLAST | 1.4.0 | Â |
BLAST | 2.2.30+ | Â |
Razers3 | 3.1.1./3.2 [13859] | Â |
MUSCLE | 3.8.31 | Â |
gsSeqTools | 2.9 (build 20130529_1641) | optional for sff conversion |
Perl | 5.16.3 | BioPerl (1.6.924) |
R | 3.1.1 | BioConductor (2.26.0) |
| Â | Â | FlowCore (1.32.0) |
| Â | Â | RMySQL (0.9-3) |
Python | 2.7.5 | numpy |
| Â | Â | matplotlib |
| Â | Â | MySQL-python |
MariaDB | 5.5.37 | Â |
git | 1.8.3.1 | Â |