EBARDenovo Files

2.0.1(Beta2) README - 20150115
======================================================================================
 * EBAR Denovo Assembler - EBARDenovo(Beta) version V2.0.1(B1)@2015/01/15
 *
 * Copyright (c) Hsueh-Ting Chu (htchu.taiwan@gmail.com)
 *
 * 4F., No.286, Defu Rd., South Dist., Taichung City 402, Taiwan.
 * All rights reserved.
 *
 * This file is a part of the EBAR Denovo Assembler.
 * The use and distribution terms for this software are covered by the
 * Common Public License 1.0 (http://opensource.org/licenses/cpl1.0.php).
 * By using this software in any fashion, you are agreeing to be bound by
 * the terms of this license. You must not remove this notice, or
 * any other, from this software.
 * 2015/01/15
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It's a new version of EBARDenovo. The new program have simplified parameters.

(0) Quick usage
Demo command with test data in the sample subdirectory:
  (Windows)   EBARDenovo sample\Samp1_R1.fq.bz2 sample\Samp1_R2.fq.bz2 sample\Samp2_R1.fq.gz sample\Samp2_R2.fq.gz -o sample.fa
  (Linux) mono EBARDenovo.exe sample/Samp1_R1.fq.bz2 sample/Samp1_R2.fq.bz2 sample/Samp2_R1.fq.gz sample/Samp2_R2.fq.gz -o sample.fa
Output files:
  (a) sample.fa : sequences of contigs
  (b) sample.csv: spreadsheet of contig information about length and coverage
  (c) sample-YYYYMMDDhhmm.log: log file of execution time and results

***The sample data are combined with reads of different lengths (100bp and 126bp) in two file formats (bz2 and gz).
***For Linux users, Linux Mint 17.1 Rebecca is the suggested distribution of Linux.

(1) Assembly for sra format. The file format of downloaded data from NCBI Sequence Read Archive is sra.
    You need the tool fastq-dump from http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software and run the command as:
    fastq-dump -I --split-files SRR100XXXX.sra

(2) Strand specific types
    The parameter "-1" indicates the sequencing reads are in RF (reverse-forward) type.
    The parameter "-2" indicates the sequencing reads are in FR (forward-reverse) type.
    Such as the assembly of a strand-specific RNA-seq data from NCBI SRA experiments ID: SRX593724 
    EBARDenovo -1 SRR1386212_1.fastq SRR1386212_2.fastq -o output.fa

(3) EBARDenovo2 admits the assembly of small contigs. For comparison of different assemblies, 
    the size of output contigs can be limited with the parameter "-c 200" while the minimal size is 200bp.
    Or, you can use the command tool ContigC200 to filter the contigs after the entire assembly job.

(4) By default, EBARDenovo2 don't output the detected chimeric segments which are not aligned into contigs.
    Th11ose detected chimeric segments can be output into the outputfile-chimera.fa with the parameter "-Q".  

(5) The small programs ContigN50 is used to report the N50 value and other statistics of an assembly.