使用部分或相关基因组序列增强RNA-Seq组装.zip

##### Contents [Overview] (#overview) [Copy right] (#copyright) [How to cite BRANCH?] (#cite) [Short Manual] (#manual) <a name="overview"/> ### Overview BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete. <a name="copyright"/> ###Copy right BRANCH is under the [Artistic License 2.0](http://opensource.org/licenses/Artistic-2.0). <a name="cite"/> ### How to cite BRANCH? If you use BRANCH, please cite the following paper: Bao E, Jiang T, Girke T (2013). BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. Bioinformatics: [epub](http://bioinformatics.oxfordjournals.org/content/29/10/1250). <a name="manual"/> ### Short manual 1. System requirements BRANCH is suitable for 32-bit or 64-bit machines with Linux operating systems. At least 4GB of system memory is recommended for assembling larger data sets. 2. Installation The [LEMON](http://lemon.cs.elte.hu/trac/lemon) graph library is required to compile and run BRANCH. The [BLAT](http://genome.ucsc.edu/FAQ/FAQblat.html) aligner is required to run BRANCH and the modified version (distributed with BRANCH) is highly recommended. * Download the .cpp file. * If LEMON is already installed in your system, execute the command line: `g++ -o BRANCH BRANCH.cpp -lemon -lpthread`; otherwise, down load LEMON, compile it, and execute: `g++ -o BRANCH -I PATH2LEMON/include BRANCH.cpp -L PATH2LEMON/bin -lpthread`. * To use the modified BLAT, put it to your $PATH: `export PATH=PATH2BLAT:$PATH`. 3. Input * Single- or paired-end RNA reads in FASTA format. * De novo transfrags assembled by any de novo RNA assembler (Velvet/Oases, Trinity, etc.). * DNA contigs assembled by any de novo DNA assembler (Velvet, ABySS, etc.) or genome/gene sequences from a closely related species. 4. Using BRANCH ``` BRANCH --read1 reads_1.fa --read2 reads_2.fa --transfrag transfrags.fa --contig contigs.fa --transcript transcripts.fa [--insertLow insertLow --insertHigh insertHigh --threshSize threshSize --threshCov threshCov --threshSplit threshSplit --threshConn threshConn --closeGap --noAlignment] ``` Inputs: --read1 is the first pair of PE RNA reads or single-end RNA reads in fasta format --read2 is the second pair of PE RNA reads in fasta format --transfrag is the de novo RNA transfrags to be extended --contig is the reference DNA contigs Output: --transcript is the extended de novo transfrags Options: --insertLow is the lower bound of insert length (highly recommended; default: 0) --insertHigh is the upper bound of insert length (highly recommended; default: 99999) --threshSize is the minimum size of a genome region that could be identified as an exon (default: 2 bp) --threshCov is the minimum coverage of a genome region that could be identified as an exon (default: 2) --threshSplit is the minimum upstream and downstream junction coverages to split a genome region into more than one exons (default: 2) --threshConn is the minimum connectivity of two exons that could be identified as a splice junction (default: 2) --closeGap closes sequencing gaps using PE read information (default: none) --noAlignment skips the initial time-consuming alignment step, if all the alignment files have been provided in tmp directory (default: none) --misassemblyRemoval detects and then breaks at or removes misassembed regions (default: none) 5. Output BRANCH outputs the transfrag file in FASTA format. It contains all the improved transfrags. 6. Important things to note * Single-end reads should have the same length and are not recommended, since the quality of single-end alignment is hard to be kept. * It is better to use related gene sequences rather than related genome sequences to greatly reduce run time and memory usage. * Though --insertLow and --insertHigh are options, they should always be specified to generate meaning result. Suppose the insert length is I, insertLow = I - 20 and insertHigh = I + 20 would be fine.