ABYSS(1)
NAME
ABYSS - assemble short reads into contigs
SYNOPSIS
ABYSS [OPTION]... FILE...
DESCRIPTION
Assemble all input files, FILE, which may be in FASTA, FASTQ, qseq,
export, SRA, SAM or BAM format and may be compressed with gz, bz2 or xz
and may be tarred.
Users wishing to run a full assembly with ABySS are recommended to use
abyss-pe as their entry point rather than the ABYSS program. abyss-pe
is a Makefile that coordinates many of the ABySS tools (including
ABYSS) in order to run the full ABySS assembly pipeline. abyss-pe is
capable of doing many things that ABYSS is not, such as leveraging the
distance information provided by paired end reads and mate pair reads.
--chastity
discard unchaste reads [default]
--no-chastity
do not discard unchaste reads
--trim-masked
trim masked bases from the ends of reads [default]
--no-trim-masked
do not trim masked bases from the ends of reads
-q, --trim-quality=THRESHOLD
trim bases from the ends of reads whose quality is less than the
threshold
-Q, --mask-quality=THRESHOLD
mask all bases in reads whose quality is less than the threshold
--standard-quality
zero quality is `!' (33)
default for FASTQ and SAM files
--illumina-quality
zero quality is `@' (64)
default for qseq and export files
-o, --out=FILE
write the contigs to FILE
-k, --kmer=KMER_SIZE
k-mer size
-t, --trim-length=TRIM_LENGTH
maximum length of dangling edges to trim
-c, --coverage=COVERAGE
remove contigs with mean k-mer coverage less than this threshold
-b, --bubbles=N
pop bubbles shorter than N bp (default: 3*k).
-b0, --no-bubbles
do not pop bubbles
-e, --erode=COVERAGE
erode bases at the ends of blunt contigs with coverage less than
this threshold
-E, --erode-strand=COVERAGE
erode bases at the ends of blunt contigs with coverage less than
this threshold on either strand
--coverage-hist=FILE
record the k-mer coverage histogram in FILE
-g, --graph=FILE
generate a graph in dot format
-s, --snp=FILE
record popped bubbles in FILE
-v, --verbose
display verbose output
--help display this help and exit
--version
output version information and exit
AUTHOR
Written by Jared Simpson and Shaun Jackman.
REPORTING BUGS
Report bugs to <abyss-users@bcgsc.ca>.
COPYRIGHT
Copyright 2015 Canada's Michael Smith Genome Sciences Centre
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
