mira-assembler

Whole Genome Shotgun and EST Sequence Assembler

The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For expressed sequence tags (ESTs) transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments. The package provides the following executables: Binaries provided: * mira: for assembly of genome sequences * miramem: estimating memory needed to assemble projects. Realised through link to mira. * convert_project: for converting project file types into other types * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some frequently used file converters (realised through links to convert_project) * scftool: set of tools useful when working with SCF trace files * fastatool: set of tools useful when working with FASTA trace files Scripts provided: * fasta2frag: fragmenting sequences into smaller, overlapping subsequences. Useful for simulating shotgun sequences. Can create subsequences in both directions (/default) and also paired-end sequences. * fastaselect: given a FASTA file (and possibly a FASTA quality file) and a file with names of reads, select the sequences from the input FASTA (and quality file) and writes them to an output FASTA * fastqselect: like fastaselect, only for FASTQ * fixACE4consed: Consed has a bug which incapacitates it from reading consensus tags in ACE files written by the MIRA assembler (and possibly other programs). This script massages an ACE file so that consed can read the consensus tags.