• 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</filename></filename></filename></filename></filename></name>