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[TOC]

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安装环境

Ubuntu18.10
BBMap_38.31

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安装过程

from the terminal window/linux shell:

$ cd (installation parent folder)

Extract the files using tar:

$ tar -xvzf BBMap_(version).tar.gz

this creates a subfolder named bbmap with the shell scripts and other necessary files.

To test the installation run stats.sh against the PhiX reference genome (included in the BBTools download):

$ (installation directory)/stats.sh in=(installation directory)/resources/phix174_ill.ref.fa.gz

A   C   G   T   N   IUPAC   Other   GC  GC_stdev
0.2399  0.2144  0.2326  0.3130  0.0000  0.0000  0.0000  0.4471  0.0000

Main genome scaffold total:             1
Main genome contig total:               1
Main genome scaffold sequence total:    0.005 MB
Main genome contig sequence total:      0.005 MB    0.000% gap
Main genome scaffold N/L50:             1/5.386 KB
Main genome contig N/L50:               1/5.386 KB
Main genome scaffold N/L90:             1/5.386 KB
Main genome contig N/L90:               1/5.386 KB
Max scaffold length:                    5.386 KB
Max contig length:                      5.386 KB
Number of scaffolds > 50 KB:            0
% main genome in scaffolds > 50 KB:     0.00%


Minimum     Number          Number          Total           Total           Scaffold
Scaffold    of              of              Scaffold        Contig          Contig  
Length      Scaffolds       Contigs         Length          Length          Coverage
--------    --------------  --------------  --------------  --------------  --------
    All                  1               1           5,386           5,386   100.00%
   5 KB                  1               1           5,386           5,386   100.00%

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BBTools

BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version 7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.

BBTools is open source and free for unlimited use, and is used regularly by DOE JGI and other institutions around the world.

The BBTools suite includes programs such as:
• bbduk – filters or trims reads for adapters and contaminants using k-mers
• bbmap – short-read aligner for DNA and RNA-seq data
• bbmerge – merges overlapping or nonoverlapping pairs into a single reads
• reformat – converts sequence files between different formats such as fastq and fasta

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问题：
1、按照教程完全一样输入命令报错

bbmerge.sh in = sample1.fq out = merged.fq outu = unmerged.fq ihist = ihist.txt
java -ea -Xmx1000m -Xms1000m -cp /opt/bbmap/current/ jgi.BBMerge in = sample1.fq out = merged.fq outu = unmerged.fq ihist = ihist.txt
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 0
    at shared.PreParser.<init>(PreParser.java:73)
    at shared.PreParser.<init>(PreParser.java:30)
    at jgi.BBMerge.<init>(BBMerge.java:304)
    at jgi.BBMerge.main(BBMerge.java:49)

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https://jgi.doe.gov/data-and-tools/bbtools/