installing mira

* download url: http://sourceforge.net/projects/mira-assembler/files/
* version: 3.2.0

$ wget http://sourceforge.net/projects/mira-assembler/files/MIRA/V3.2.0/mira_3.2.0_prod_linux-gnu_x86_64_static.tar.bz2/download
$ bunzip2 mira_3.2.0_prod_linux-gnu_x86_64_static.tar.bz2
$ tar xvf mira_3.2.0_prod_linux-gnu_x86_64_static.tar
$ cd mira_3.2.0_prod_linux-gnu_x86_64_static/

* All the executables are in bin directory
* Export the path to bin to bashrc

$ vim ~/.bashrc
export PATH=$PATH:/path/to/mira/bin
$ source ~/.bashrc
$ mira
...

[edit] Instructions

* Open the index.html file present in docs folder on firefox.

[edit] Usage

mira \
[-project=]
[--job=arguments]
[-fasta[=] | -fastq[=] | -caf[=] | -phd[=]] [-notraceinfo] [-noclipping[=...]] [-highlyrepetitive] [-lowqualitydata] [-highqualitydata] [-params=] [-GENERAL:arguments]
[-STRAIN/BACKBONE:arguments]
[-ASSEMBLY:arguments]
[-DATAPROCESSING:arguments]
[-CLIPPING:arguments]
[-SKIM:arguments]
[-ALIGN:arguments]
[-CONTIG:arguments]
[-EDIT:arguments]
[-MISC:arguments]
[-DIRECTORY:arguments]
[-FILENAME:arguments]
[-OUTPUT:arguments]
[COMMON_SETTINGS | SANGER_SETTINGS | 454_SETTINGS | SOLEXA_SETTINGS | SOLID_SETTINGS]


ESTs (simulated)

* Generate a genome of 1,000,000 length
* Generated ESTs of length 500-800 bp for the above genome
* Around 10,000 ESTs were generated and stored in the file est.fasta

$ mira --project=EST --job=denovo,genome,normal,454 -fasta=est.fasta -SK:mnr=yes:nrr=10 454_SETTINGS -LR:wqf=no -LR:mxti=no -AS:epoq=no >&log_assembly.txt
$ cd EST_assembly/
$ ls -R
.:
EST_d_chkpt EST_d_info EST_d_log EST_d_results

./EST_d_chkpt:
passInfo.txt readpool.maf

./EST_d_info:
EST_info_assembly.txt EST_info_consensustaglist.txt EST_info_contigstats.txt EST_info_readrepeats.lst
EST_info_callparameters.txt EST_info_contigreadlist.txt EST_info_debrislist.txt EST_info_readtaglist.txt

./EST_d_log:
EST_error_reads_invalid EST_info_reads_tooshort EST_out_pass.2.caf
EST_info_consensustaglist.1.txt EST_info_readtaglist.1.txt EST_out_pass.3.caf
EST_info_consensustaglist.2.txt EST_info_readtaglist.2.txt EST_readpoolinfo.lst
EST_info_consensustaglist.3.txt EST_info_readtaglist.3.txt hashstat.bin
EST_info_contigreadlist_pass.1.txt EST_int_clippings.0.txt miralog.ads_pass.4.adsfacts
EST_info_contigreadlist_pass.2.txt EST_int_normalisedskims_pass.4.bin miralog.ads_pass.4.adsfacts.pclusters
EST_info_contigreadlist_pass.3.txt EST_int_posmatchc_pass.4.lst miralog.ads_pass.4.complement
EST_info_contigstats_pass.1.txt EST_int_posmatchc_pass.4.lst.reduced miralog.ads_pass.4.forward
EST_info_contigstats_pass.2.txt EST_int_posmatchf_pass.4.lst miralog.ads_pass.4.reject
EST_info_contigstats_pass.3.txt EST_int_posmatchf_pass.4.lst.reduced miralog.noqualities
EST_info_debrislist_pass.1.txt EST_int_posmatch_megahubs_pass.4.lst miralog.usedids
EST_info_debrislist_pass.2.txt EST_int_posmatch_multicopystat_preassembly.0.txt
EST_info_debrislist_pass.3.txt EST_out_pass.1.caf

./EST_d_results:
EST_out.ace EST_out.maf EST_out.padded.fasta.qual EST_out.unpadded.fasta EST_out.wig
EST_out.caf EST_out.padded.fasta EST_out.tcs EST_out.unpadded.fasta.qual

[edit] Inference

* Snippet of some of the information in EST_d_info/EST_info_assembly.txt

..
..
Length assessment:
------------------
Number of contigs: 106
Total consensus: 944829
Largest contig: 36580
N50 contig size: 13625
N90 contig size: 5366
N95 contig size: 2945
..
..

* Number of contigs in EST_out.unpadded.fasta and EST_out.padded.fasta

$ grep -c '>' ./EST_d_results/EST_out.unpadded.fasta
107