pandaseq-software
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
pandaseq-software [2014/10/07 13:44] – joguya | pandaseq-software [2014/12/08 09:27] (current) – [Installation Notes] joguya | ||
---|---|---|---|
Line 1: | Line 1: | ||
====== Pandaseq ====== | ====== Pandaseq ====== | ||
- | Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | ||
+ | Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. | ||
- | ===== Information | + | ===== Pandaseq 2.7 ===== |
+ | Information | ||
* Version: 2.7 | * Version: 2.7 | ||
* Added: October, 2014 | * Added: October, 2014 | ||
Line 9: | Line 10: | ||
- | ===== Usage ===== | + | ==== Usage ==== |
=== Show available version === | === Show available version === | ||
+ | |||
* < | * < | ||
- | === Show manpages === | + | === Show manpages === |
* Load pandaseq module: < | * Load pandaseq module: < | ||
man pandaseq</ | man pandaseq</ | ||
- | ===== Installation | + | ==== Installation ==== |
* clone repo from [[https:// | * clone repo from [[https:// | ||
git clone https:// | git clone https:// | ||
Line 58: | Line 60: | ||
pandaseq -h | pandaseq -h | ||
man pandaseq | man pandaseq | ||
+ | </ | ||
+ | |||
+ | ===== Pandaseq 2.8.1 ===== | ||
+ | Information: | ||
+ | * Version: 2.8.1 | ||
+ | * Added: December, 2014 | ||
+ | * Link: https:// | ||
+ | |||
+ | changelog: | ||
+ | * Add a plugin to display overlaps examined | ||
+ | * Add -D flag to add a penalty for shifting primers | ||
+ | * Added UPARSE algorithm | ||
+ | * Add FastqJoin algorithm | ||
+ | * Add FLASH algorithm | ||
+ | * Add Sitch algorithm | ||
+ | * Fix bug causing spurious "no sequences" | ||
+ | * Issue an error if the command line arguments have UTF-8 characters | ||
+ | * Remove min_readqscore since it doesn' | ||
+ | * Sanity check sequence length after primer stripping | ||
+ | |||
+ | |||
+ | ==== Installation Notes ==== | ||
+ | * Download pandaseq 2.8.1, create version specific dir in / | ||
+ | wget https:// | ||
+ | tar -xvf pandaseq-v2.8.1.tar.gz | ||
+ | cd pandaseq-v2.8.1 | ||
+ | sudo mkdir / | ||
+ | sudo chown -R joguya: | ||
+ | ./ | ||
+ | ./configure --prefix=/ | ||
+ | make | ||
+ | make install | ||
+ | sudo chown -R root:root / | ||
+ | </ | ||
+ | |||
+ | * pandaseq/ | ||
+ | #%Module1.0 | ||
+ | ##################################################################### | ||
+ | ## | ||
+ | ## Pandaseq Modulefile | ||
+ | ## By James Oguya, j.oguya@cgiar.org | ||
+ | ## December, 2014 | ||
+ | ## | ||
+ | |||
+ | set appname | ||
+ | set version | ||
+ | set prefix | ||
+ | set exec_prefix | ||
+ | set url " | ||
+ | set msg " | ||
+ | |||
+ | module-whatis $msg | ||
+ | |||
+ | proc ModulesHelp { } { | ||
+ | puts stderr " | ||
+ | } | ||
+ | |||
+ | conflict | ||
+ | |||
+ | prepend-path | ||
+ | prepend-path | ||
</ | </ |
pandaseq-software.1412689446.txt.gz · Last modified: 2014/10/07 13:44 by joguya