How do I install MAQ software on Ubuntu?

Question

[melissachua90]

I want to run the maq software on Ubuntu. It can be downloaded from sourceforge:

https://sourceforge.net/projects/maq/

I tried to install the software using:

cd mapass2-0.3.1_i386-win32/

./configure; make; make install

Traceback:

-bash: ./configure: No such file or directory

The file seems to indicate that its a win32 software. Where do I get a Linux version?

[Pierre Lindenbaum]

it looks like the zip contains a pre-compiled software...

  Length      Date    Time    Name
---------  ---------- -----   ----
        0  2007-05-11 13:04   mapass2-0.3.1_i386-win32/
     4074  2007-05-11 13:04   mapass2-0.3.1_i386-win32/farm-run.pl
   146944  2007-05-11 13:03   mapass2-0.3.1_i386-win32/mapass2.exe
     5043  2007-05-11 13:04   mapass2-0.3.1_i386-win32/mapass2.pl
---------                     -------
   156061                     4 files

Answer 1

[Mensur Dlakic]

Not sure that sequencing simulator written in 2007 is the best choice here.

I suggest you try ART as there are compiled binaries available. There are simulators for several sequencing technologies. A brief summary of commands to generate Illumina-like reads:

 1) single-end read simulation
        art_illumina -ss HS25 -sam -i reference.fa -l 150 -f 10 -o single_dat

 2) paired-end read simulation
       art_illumina -ss HS25 -sam -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_dat

 3) mate-pair read simulation
       art_illumina -ss HS10 -sam -i reference.fa -mp -l 100 -f 20 -m 2500 -s 50 -o matepair_dat

 4) amplicon sequencing simulation with 5' end single-end reads
        art_illumina -ss GA2 -amp -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_5end_dat

 5) amplicon sequencing simulation with paired-end reads
       art_illumina -ss GA2 -amp -p -sam -na -i amp_reference.fa -l 50 -f 10 -o amplicon_pair_dat

 6) amplicon sequencing simulation with matepair reads
       art_illumina -ss MSv1 -amp -mp -sam -na -i amp_reference.fa -l 150 -f 10 -o amplicon_mate_dat

 7) generate an extra SAM file with zero-sequencing errors for a paired-end read simulation
       art_illumina -ss HSXn -ef -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_twosam_dat

 8) reduce the substitution error rate to one 10th of the default profile
       art_illumina -i reference.fa -qs 10 -qs2 10 -l 50 -f 10 -p -m 500 -s 10 -sam -o reduce_error

 9) turn off the masking of genomic regions with unknown nucleotides 'N'
       art_illumina -ss HS20 -nf 0  -sam -i reference.fa -p -l 100 -f 20 -m 200 -s 10 -o paired_nomask

 10) masking genomic regions with >=5 'N's within the read length 50
       art_illumina -ss HSXt -nf 5 -sam -i reference.fa -p -l 150 -f 20 -m 200 -s 10 -o paired_maskN5

[GenoMax]

maq was the precursor of bwa, as I recall. In fact the link that OP has posted points to bwa v.0.5.0. maq is an aligner/assmber (LINK) and not a read simulator.

[Mensur Dlakic]

Thanks, that was my bad. I thought it was the same question as here, which is where that answer above applies.

Answer 2

[Charles Plessy]

sudo apt install maq, but I agree that using a newer software will be wiser.