Palmapper and Oqtans

Oqtans looks like an interesting tool for analysing RNA-seq data based on Galaxy framework. Unfortunately the server is down. But it did point to another mapping tool which I am curious to try out PALmapper. What piqued my interest is this in the abstract
"align around 7 million reads per hour on a single AMD CPU core (similar speed as TopHat [3]). Our study for C. elegans furthermore shows that PALMapperPALMapper is considerably more accurate than TopHat (47% and 81%, respectively)." predicts introns with very high sensitivity (72%) and specificity (82%) when using the annotation as ground truth.

Sort 1 Terabyte of data in a 60 seconds?

UC San Diego Computer scientists did that according to HPCwire.

"SAN DIEGO, July 27 -- Computer scientists from the University of California, San Diego broke "the terabyte barrier" -- and set a new world record -- when they sorted more than one terabyte of data (1,000 gigabytes or 1 million megabytes) in just 60 seconds on a computing cluster at Calit2. During this 2010 "Sort Benchmark" competition -- the "World Cup of data sorting" -- the computer scientists from the UC San Diego Jacobs School of Engineering also tied a world record for fastest data sorting rate. They sorted one trillion data records in 172 minutes – and did so using just a quarter of the computing resources of the other record holder....."

Gosh and I felt I was having trouble sorting mere gigabytes of data ...


"Sorting is also an interesting proxy for a whole bunch of other data processing problems. Generally, sorting is a great way to measure how fast you can read a lot of data off a set of disks, do some basic processing on it, shuffle it around a network and write it to another set of disks," explained Rasmussen. "Sorting puts a lot of stress on the entire input/output subsystem, from the hard drives and the networking hardware to the operating system and application software."


 I would love to find out how you can sort items bigger than ramspace efficiently and see how they can be implemented on bioinformatics problems.


Do check out http://sortbenchmark.org/
They have various metrics for sorting most of which I had never thought of before!
I love the category of PennySort in particular!

Metric: Amount of data that can be sorted for a penny's worth of system time.
Originally defined in AlphaSort paper.

There's also JouleSort

 Metric: Amount of energy required to sort either 10⁸, 10⁹ or 10¹⁰ records (10 GB, 100 GB or 1 TB).
Originally defined in JouleSort paper.

Google Chrome in CentOS? You will have to wait

Rant warning:
Gah!
Another crippling experience of working with CentOS.

I still can't install chrome despite google having an official linux port due to an outdated package (lsb) on CentOS 5.4

Others are having the same issues.

Shiny new tool to index NGS reads G-SQZ

This is a long over due tool for those trying to do non-typical analysis with your reads.
Finally you can index and compress your NGS reads

http://www.ncbi.nlm.nih.gov/pubmed/20605925

Bioinformatics. 2010 Jul 6. [Epub ahead of print]
G-SQZ: Compact Encoding of Genomic Sequence and Quality Data.

Tembe W, Lowey J, Suh E.

Translational Genomics Research Institute, 445 N 5th Street, Phoenix, AZ 85004, USA.
Abstract

SUMMARY: Large volumes of data generated by high-throughput sequencing instruments present non-trivial challenges in data storage, content access, and transfer. We present G-SQZ, a Huffman coding-based sequencing-reads specific representation scheme that compresses data without altering the relative order. G-SQZ has achieved from 65% to 81% compression on benchmark datasets, and it allows selective access without scanning and decoding from start. This paper focuses on describing the underlying encoding scheme and its software implementation, and a more theoretical problem of optimal compression is out of scope. The immediate practical benefits include reduced infrastructure and informatics costs in managing and analyzing large sequencing data. AVAILABILITY: http://public.tgen.org/sqz Academic/non-profit: Source: available at no cost under a non-open-source license by requesting from the web-site; Binary: available for direct download at no cost. For-Profit: Submit request for for-profit license from the web-site. CONTACT: Waibhav Tembe (wtembe@tgen.org).

read the discussion thread in seqanswers for more tips and benchmarks

I am not affliated with the author btw

the nuts and bolts behind ABI's SAET

I really do not like to use tools that I have no idea what they are trying to do. 

ABI's SAET SOLiD™ Accuracy Enhancer Tool (SAET) is a one example that had extremely brief documentation except what it promised to do 

• The SOLiD™ Accuracy Enhancer Tool (SAET) uses raw data generated by SOLiD™ Analyzer to correct miscalls within reads prior to mapping or contig assembly.  
  
• Use of SAET, on various datasets of whole or sub-genomes of < 200 Mbp in size and of varying complexities, readlengths, and sequence coverages, has demonstrated improvements in mapping, SNP calling, and de novo assembly results.
  
• For denovo applications, the tool reduces miscall rate substantially
  
  Recently attended an ABI's talk and finally someone explained it in a nice diagram. It is akin to Softgenetic's condensation tool.( I made the link ). Basically, it groups reads by similarity and where they find a mismatch that is not supported by high quality reads they correct the low quality read to reach a 'consensus'. I see it as a batch correction of sequencing errors which one can typically do by eye (for small regions). This correction isn't without its flaws. I now understand why such an error correction isn't implemented on the instrument. And is presented as a user choice. My rough experience with this tool is that it increases mapping by ~ 10% how this 10% would affect your results is debatable.
  

A Boycott for NPG journals?

NPG as in Nature Publishing Group for those not in the know, this includes the journal Nature. What might have sparked off this?
An impending price increase of 400% for journal subscription.

Michael Eisen, nailed it down it his blog post.
I totally agree with his view especially how he describes the situation as:
"Only one thing — short of outright insanity — can lead a company to think they can get away with this kind of behavior: a monopoly. And it is the monopolistic, and grossly unfair and irrational, business model that NPG and most other scientific publishers employ that should be the real target of any organized action from UC faculty."

Jonathan Eisen also has interesting things posted here

I think the price increase might be a good move to persuade researchers to use soft copies of journals instead of having to resorting to print. But as Michael rightly points out. It shouldn't be an issue of price. And price increase in this climate, I think NPG might be making a wrong move here.

What are your thoughts? Would you adhere to such a boycott if your department is against the idea?

Do you talk awk ?

Neat file! I have one of my own recipes but it pales in comparison to this .. anyway.. is it possible to write 2 lines of awk code? rofl.

HANDY ONE-LINE SCRIPTS FOR AWK                               30 April 2008
Compiled by Eric Pement - eric [at] pement.org               version 0.27

Latest version of this file (in English) is usually at:
   http://www.pement.org/awk/awk1line.txt

This file will also be available in other languages:
   Chinese  - http://ximix.org/translation/awk1line_zh-CN.txt   

USAGE:

   Unix: awk '/pattern/ {print "$1"}'    # standard Unix shells
DOS/Win: awk '/pattern/ {print "$1"}'    # compiled with DJGPP, Cygwin
         awk "/pattern/ {print \"$1\"}"  # GnuWin32, UnxUtils, Mingw

Note that the DJGPP compilation (for DOS or Windows-32) permits an awk
script to follow Unix quoting syntax '/like/ {"this"}'. HOWEVER, if the
command interpreter is CMD.EXE or COMMAND.COM, single quotes will not
protect the redirection arrows (<, >) nor do they protect pipes (|).
These are special symbols which require "double quotes" to protect them
from interpretation as operating system directives. If the command
interpreter is bash, ksh or another Unix shell, then single and double
quotes will follow the standard Unix usage.

Users of MS-DOS or Microsoft Windows must remember that the percent
sign (%) is used to indicate environment variables, so this symbol must
be doubled (%%) to yield a single percent sign visible to awk.

If a script will not need to be quoted in Unix, DOS, or CMD, then I
normally omit the quote marks. If an example is peculiar to GNU awk,
the command 'gawk' will be used. Please notify me if you find errors or
new commands to add to this list (total length under 65 characters). I
usually try to put the shortest script first. To conserve space, I
normally use '1' instead of '{print}' to print each line. Either one
will work.

FILE SPACING:

 # double space a file
 awk '1;{print ""}'
 awk 'BEGIN{ORS="\n\n"};1'

 # double space a file which already has blank lines in it. Output file
 # should contain no more than one blank line between lines of text.
 # NOTE: On Unix systems, DOS lines which have only CRLF (\r\n) are
 # often treated as non-blank, and thus 'NF' alone will return TRUE.
 awk 'NF{print $0 "\n"}'

 # triple space a file
 awk '1;{print "\n"}'

NUMBERING AND CALCULATIONS:

 # precede each line by its line number FOR THAT FILE (left alignment).
 # Using a tab (\t) instead of space will preserve margins.
 awk '{print FNR "\t" $0}' files*

 # precede each line by its line number FOR ALL FILES TOGETHER, with tab.
 awk '{print NR "\t" $0}' files*

 # number each line of a file (number on left, right-aligned)
 # Double the percent signs if typing from the DOS command prompt.
 awk '{printf("%5d : %s\n", NR,$0)}'

 # number each line of file, but only print numbers if line is not blank
 # Remember caveats about Unix treatment of \r (mentioned above)
 awk 'NF{$0=++a " :" $0};1'
 awk '{print (NF? ++a " :" :"") $0}'

 # count lines (emulates "wc -l")
 awk 'END{print NR}'

 # print the sums of the fields of every line
 awk '{s=0; for (i=1; i<=NF; i++) s=s+$i; print s}'

 # add all fields in all lines and print the sum
 awk '{for (i=1; i<=NF; i++) s=s+$i}; END{print s}'

 # print every line after replacing each field with its absolute value
 awk '{for (i=1; i<=NF; i++) if ($i < 0) $i = -$i; print }'
 awk '{for (i=1; i<=NF; i++) $i = ($i < 0) ? -$i : $i; print }'

 # print the total number of fields ("words") in all lines
 awk '{ total = total + NF }; END {print total}' file

 # print the total number of lines that contain "Beth"
 awk '/Beth/{n++}; END {print n+0}' file

 # print the largest first field and the line that contains it
 # Intended for finding the longest string in field #1
 awk '$1 > max {max=$1; maxline=$0}; END{ print max, maxline}'

 # print the number of fields in each line, followed by the line
 awk '{ print NF ":" $0 } '

 # print the last field of each line
 awk '{ print $NF }'

 # print the last field of the last line
 awk '{ field = $NF }; END{ print field }'

 # print every line with more than 4 fields
 awk 'NF > 4'

 # print every line where the value of the last field is > 4
 awk '$NF > 4'

STRING CREATION:

 # create a string of a specific length (e.g., generate 513 spaces)
 awk 'BEGIN{while (a++<513) s=s " "; print s}'

 # insert a string of specific length at a certain character position
 # Example: insert 49 spaces after column #6 of each input line.
 gawk --re-interval 'BEGIN{while(a++<49)s=s " "};{sub(/^.{6}/,"&" s)};1'

ARRAY CREATION:

 # These next 2 entries are not one-line scripts, but the technique
 # is so handy that it merits inclusion here.
 
 # create an array named "month", indexed by numbers, so that month[1]
 # is 'Jan', month[2] is 'Feb', month[3] is 'Mar' and so on.
 split("Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec", month, " ")

 # create an array named "mdigit", indexed by strings, so that
 # mdigit["Jan"] is 1, mdigit["Feb"] is 2, etc. Requires "month" array
 for (i=1; i<=12; i++) mdigit[month[i]] = i

TEXT CONVERSION AND SUBSTITUTION:

 # IN UNIX ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 awk '{sub(/\r$/,"")};1'   # assumes EACH line ends with Ctrl-M

 # IN UNIX ENVIRONMENT: convert Unix newlines (LF) to DOS format
 awk '{sub(/$/,"\r")};1'

 # IN DOS ENVIRONMENT: convert Unix newlines (LF) to DOS format
 awk 1

 # IN DOS ENVIRONMENT: convert DOS newlines (CR/LF) to Unix format
 # Cannot be done with DOS versions of awk, other than gawk:
 gawk -v BINMODE="w" '1' infile >outfile

 # Use "tr" instead.
 tr -d \r outfile            # GNU tr version 1.22 or higher

 # delete leading whitespace (spaces, tabs) from front of each line
 # aligns all text flush left
 awk '{sub(/^[ \t]+/, "")};1'

 # delete trailing whitespace (spaces, tabs) from end of each line
 awk '{sub(/[ \t]+$/, "")};1'

 # delete BOTH leading and trailing whitespace from each line
 awk '{gsub(/^[ \t]+|[ \t]+$/,"")};1'
 awk '{$1=$1};1'           # also removes extra space between fields

 # insert 5 blank spaces at beginning of each line (make page offset)
 awk '{sub(/^/, "     ")};1'

 # align all text flush right on a 79-column width
 awk '{printf "%79s\n", $0}' file*

 # center all text on a 79-character width
 awk '{l=length();s=int((79-l)/2); printf "%"(s+l)"s\n",$0}' file*

 # substitute (find and replace) "foo" with "bar" on each line
 awk '{sub(/foo/,"bar")}; 1'           # replace only 1st instance
 gawk '{$0=gensub(/foo/,"bar",4)}; 1'  # replace only 4th instance
 awk '{gsub(/foo/,"bar")}; 1'          # replace ALL instances in a line

 # substitute "foo" with "bar" ONLY for lines which contain "baz"
 awk '/baz/{gsub(/foo/, "bar")}; 1'

 # substitute "foo" with "bar" EXCEPT for lines which contain "baz"
 awk '!/baz/{gsub(/foo/, "bar")}; 1'

 # change "scarlet" or "ruby" or "puce" to "red"
 awk '{gsub(/scarlet|ruby|puce/, "red")}; 1'

 # reverse order of lines (emulates "tac")
 awk '{a[i++]=$0} END {for (j=i-1; j>=0;) print a[j--] }' file*

 # if a line ends with a backslash, append the next line to it (fails if
 # there are multiple lines ending with backslash...)
 awk '/\\$/ {sub(/\\$/,""); getline t; print $0 t; next}; 1' file*

 # print and sort the login names of all users
 awk -F ":" '{print $1 | "sort" }' /etc/passwd

 # print the first 2 fields, in opposite order, of every line
 awk '{print $2, $1}' file

 # switch the first 2 fields of every line
 awk '{temp = $1; $1 = $2; $2 = temp}' file

 # print every line, deleting the second field of that line
 awk '{ $2 = ""; print }'

 # print in reverse order the fields of every line
 awk '{for (i=NF; i>0; i--) printf("%s ",$i);print ""}' file

 # concatenate every 5 lines of input, using a comma separator
 # between fields
 awk 'ORS=NR%5?",":"\n"' file

SELECTIVE PRINTING OF CERTAIN LINES:

 # print first 10 lines of file (emulates behavior of "head")
 awk 'NR < 11'

 # print first line of file (emulates "head -1")
 awk 'NR>1{exit};1'

  # print the last 2 lines of a file (emulates "tail -2")
 awk '{y=x "\n" $0; x=$0};END{print y}'

 # print the last line of a file (emulates "tail -1")
 awk 'END{print}'

 # print only lines which match regular expression (emulates "grep")
 awk '/regex/'

 # print only lines which do NOT match regex (emulates "grep -v")
 awk '!/regex/'

 # print any line where field #5 is equal to "abc123"
 awk '$5 == "abc123"'

 # print only those lines where field #5 is NOT equal to "abc123"
 # This will also print lines which have less than 5 fields.
 awk '$5 != "abc123"'
 awk '!($5 == "abc123")'

 # matching a field against a regular expression
 awk '$7  ~ /^[a-f]/'    # print line if field #7 matches regex
 awk '$7 !~ /^[a-f]/'    # print line if field #7 does NOT match regex

 # print the line immediately before a regex, but not the line
 # containing the regex
 awk '/regex/{print x};{x=$0}'
 awk '/regex/{print (NR==1 ? "match on line 1" : x)};{x=$0}'

 # print the line immediately after a regex, but not the line
 # containing the regex
 awk '/regex/{getline;print}'

 # grep for AAA and BBB and CCC (in any order on the same line)
 awk '/AAA/ && /BBB/ && /CCC/'

 # grep for AAA and BBB and CCC (in that order)
 awk '/AAA.*BBB.*CCC/'

 # print only lines of 65 characters or longer
 awk 'length > 64'

 # print only lines of less than 65 characters
 awk 'length < 64'

 # print section of file from regular expression to end of file
 awk '/regex/,0'
 awk '/regex/,EOF'

 # print section of file based on line numbers (lines 8-12, inclusive)
 awk 'NR==8,NR==12'

 # print line number 52
 awk 'NR==52'
 awk 'NR==52 {print;exit}'          # more efficient on large files

 # print section of file between two regular expressions (inclusive)
 awk '/Iowa/,/Montana/'             # case sensitive

SELECTIVE DELETION OF CERTAIN LINES:

 # delete ALL blank lines from a file (same as "grep '.' ")
 awk NF
 awk '/./'

 # remove duplicate, consecutive lines (emulates "uniq")
 awk 'a !~ $0; {a=$0}'

 # remove duplicate, nonconsecutive lines
 awk '!a[$0]++'                     # most concise script
 awk '!($0 in a){a[$0];print}'      # most efficient script

CREDITS AND THANKS:

Special thanks to the late Peter S. Tillier (U.K.) for helping me with
the first release of this FAQ file, and to Daniel Jana, Yisu Dong, and
others for their suggestions and corrections.

For additional syntax instructions, including the way to apply editing
commands from a disk file instead of the command line, consult:

  "sed & awk, 2nd Edition," by Dale Dougherty and Arnold Robbins
  (O'Reilly, 1997)

  "UNIX Text Processing," by Dale Dougherty and Tim O'Reilly (Hayden
  Books, 1987)

  "GAWK: Effective awk Programming," 3d edition, by Arnold D. Robbins
  (O'Reilly, 2003) or at http://www.gnu.org/software/gawk/manual/

To fully exploit the power of awk, one must understand "regular
expressions." For detailed discussion of regular expressions, see
"Mastering Regular Expressions, 3d edition" by Jeffrey Friedl (O'Reilly,
2006).

The info and manual ("man") pages on Unix systems may be helpful (try
"man awk", "man nawk", "man gawk", "man regexp", or the section on
regular expressions in "man ed").

USE OF '\t' IN awk SCRIPTS: For clarity in documentation, I have used
'\t' to indicate a tab character (0x09) in the scripts.  All versions of
awk should recognize this abbreviation.

#---end of file---