Hi!

I was wondering what you recommend for structuring sets of forward and reverse reads to provide to MAC when read length and insert size are variable.

Our PE insert size is ~200 bp but MP insert sizes vary from 500-2000 bp. Should all of these reads be combined into single forward and reverse sets? if so, what should I provide for insert size and read length? Or should I create sets of forward and reverse reads based on read length and insert size? If so, how should I structure the command line to run MAC?

I also was wondering, will MAC work for animal genomes? Or is designed more for bacteria and viruses and/or other smaller genomes?

Thank you for your help!

There is a problem with the MAC installation when I use the recommended command g++ MAC2.0.cpp -o MAC2.0，
The error shows：

MAC2.0.cpp: In function ‘Vi findNumbers(std::__cxx11::string&, Vi&)’:
MAC2.0.cpp:82:15: error: ‘i’ does not name a type
     for (auto i: inc) res.pb(numarr[i-1]);
               ^
MAC2.0.cpp:83:5: error: expected ‘;’ before ‘return’
     return res;
     ^
MAC2.0.cpp:83:5: error: expected primary-expression before ‘return’
MAC2.0.cpp:83:5: error: expected ‘;’ before ‘return’
MAC2.0.cpp:83:5: error: expected primary-expression before ‘return’
MAC2.0.cpp:83:5: error: expected ‘)’ before ‘return’
MAC2.0.cpp: In function ‘void buildContig()’:
MAC2.0.cpp:103:28: error: in C++98 ‘inc’ must be initialized by constructor, not by ‘{...}’
     Vi inc = {1,2,3,4,13,14};
                            ^
MAC2.0.cpp:103:28: error: could not convert ‘{1, 2, 3, 4, 13, 14}’ from ‘<brace-enclosed initializer list>’ to ‘Vi {aka std::vector<int>}’
MAC2.0.cpp:108:21: warning: extended initializer lists only available with -std=c++11 or -std=gnu++11
         gene.pb(Gene{min(align_info[2],align_info[3]), max(align_info[2],align_info[3]), min(align_info

But when I use g++ -std=c++11 -std=gnu++11 MAC2.0.cpp -o MAC2.0,it works.The MAC is available.
So ,the recommended installation command can be replaced by g++ -std=c++11 -std=gnu++11 MAC2.0.cpp -o MAC2.0

Hello,
I am interesting with your approach but I don't know how to run it.
Can it merge contigs from a single contig file or we have to give a reference?
Cheers

To whom it may concern,

I wanted to reconcile 6 assemblies using MAC. I can use the current README to reconcile two assemblies (query and reference) but based on my understanding of the paper it is possible to add more assemblies, correct? Can you show the correct script to use to have MAC2.0 work for more than 2 assemblies?

Hello,

I noticed that this repo is missing a license while intending to put in a pull request because I found a couple of bugs. This indicates that the rights of the code are all reserved.

Having the code publicly available as indicated in the publication makes me think the intention for this source code is to be open source. Even if this is not the case, I think it would be best to understand what limitations we have when using this software.

Could the maintainers please add a license?

I am trying to merging two assemblies, but it is showing parameters format error. what does exactly that error message mean?
my code: /data/mito_assembly/blast_nuc_mito_assembly/57/MAC2/MAC2.0 1.fasta 2.fasta

Dear all, I am running the following command for merging assemblies:
php ./MAC.php ~/assembly_1 ~/assembly_2 ~/IlluminaSRs_paired1.fastq ~/IlluminaSRs_paired2.fastq ~/MAC_output/

ERROR: Could not parse delta file, ~/MAC_output//Mix2.delta error no: 400
ERROR: Could not parse delta file, ~/MAC_output//Mix2.filter error no: 402

How could I solve it?

Hello there

Decided to use your program to merge some bacterial assmeblies,
here is the current command I'm using and returns the "error: Contig File does not exist!" message

./MAC2.0 contig-140.fa final_contigs.fa
I've completed their names with Tab

I'm following the usage example

g++ MAC2.0.cpp -o MAC2.0

MAC2.0 <contig_query.fa> <contig_reference.fa>

Could you elaborate a bit better on the "The input files need to be placed in the ./input folder.

The output file will be output to the ./output folder."

Do I have to create these folders?

Thank you in advance

Hi, I can't really understand how to merge multiple contigs from different assembly.
I cannot find any manual to use this program and I need some help
thanks in advance, Maria

mufeeda@mufeeda-Aspire-A514-53:~/Desktop/MAC-2.1$ ./MAC2.0 '/home/mufeeda/Desktop/MAC-2.1/input/contigs.fa' '/home/mufeeda/Desktop/MAC-2.1/input/outputGraph.fa'
error: Contig File does not exist
I have put both query and ref fasta in input folder and run the MAC. Still it is showing error ' Contig file doesnot exist'. Please help me to rectify this issue
Thank you in advance