Software for practical on genome assembly - Jean-François

caseywdunn commented 8 years ago

Here is the list of the programs I would need to have installed on the Amazon computers the students will use for my practical on genome assembly (Wednesday 1st June):

BioPieces (https://github.com/maasha/biopieces/wiki/Installation)
ART (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/)
Celera Assembler (http://wgs-assembler.sourceforge.net/wiki/index.php?title=Main_Page) with the fastqtoCA utility (http://wgs-assembler.sourceforge.net/wiki/index.php/FastqToCA)
IDBA_UD (http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/) with the fq2fa utility
Platanus (http://platanus.bio.titech.ac.jp/)
MIRA (https://sourceforge.net/projects/mira-assembler/)
QUAST (http://quast.bioinf.spbau.ru/)
xmgrace (ftp://plasma-gate.weizmann.ac.il/pub/grace/)
LibreOffice (https://www.libreoffice.org/)

caseywdunn commented 8 years ago

Also SPAdes (http://bioinf.spbau.ru/spades)

jflot commented 8 years ago

Here is what I did to install the various programs:

for IDBA_UD: wget http://hku-idba.googlecode.com/files/idba-1.1.1.tar.gz; tar -xvzf idba-1.1.1.tar.gz; cd idba-1.1.1/; sed -i 's/kMaxShortSequence = 128/kMaxShortSequence = 16384/' src/sequence/short_sequence.h; ./configure; make; cp fq2fa ~/bin; cp idba_ud ~/bin; cp raw_n50 ~/bin; cp sim_reads ~/bin

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