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Home modified by Yun Heo

Yun Heo — Sat, 03 Dec 2016 06:35:41 -0000

--- v34
+++ v35
@@ -142,9 +142,10 @@

 #### Publications ####
 Yun Heo, Xiao-Long Wu, Deming Chen, Jian Ma, Wen-Mei Hwu (2014). BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics, 30 (10), 1354-1362. doi: 10.1093/bioinformatics/btu030
+
 Yun Heo, Anand Ramachandran, Wen-Mei Hwu, Jian Ma, Deming Chen (2016). BLESS 2: accurate, memory-efficient and fast error correction method. Bioinformatics, 32 (15): 2369-2371. 10.1093/bioinformatics/btw146
 



 #### Bug Reports ####
-Yun Heo <yunheo1 at illinois.edu>
+Anand Ramachandran <aramach4 at illinois.edu>

Home modified by Yun Heo

Yun Heo — Sat, 03 Dec 2016 06:32:38 -0000

Home modified by Yun Heo

Yun Heo — Sat, 03 Dec 2016 06:32:08 -0000

--- v32
+++ v33
@@ -142,6 +142,7 @@

 #### Publications ####
 Yun Heo, Xiao-Long Wu, Deming Chen, Jian Ma, Wen-Mei Hwu (2014). BLESS: Bloom filter-based error correction solution for high-throughput sequencing reads. Bioinformatics, 30 (10), 1354-1362. doi: 10.1093/bioinformatics/btu030
+Yun Heo, Anand Ramachandran, Wen-Mei Hwu, Jian Ma, Deming Chen (2016). BLESS 2: accurate, memory-efficient and fast error correction method. Bioinformatics, 32 (15): 2369-2371. 10.1093/bioinformatics/btw146

Home modified by Yun Heo

Yun Heo — Wed, 10 Jun 2015 16:07:01 -0000

--- v31
+++ v32
@@ -63,6 +63,9 @@
 Runtime is improved by 10%.
 All the dependent libraries are included.
 Errors in compiling pigz are fixed.
+
+V1.02: 06/10/2015
+A bug in single-end reads with many Ns is fixed.
 



 #### System Requirements ####

Home modified by Yun Heo

Yun Heo — Wed, 10 Jun 2015 03:39:36 -0000

--- v30
+++ v31
@@ -31,7 +31,7 @@
 V0.17: 06/03/2014
 A bug in setting the maximum allowed Ns for paired reads is fixed.

-V0.20: 10/16/2014
+V0.20: 10/16/2014 (Preliminary release of BLESS 2)
 BLESS is parallelized using OpenMP and MPI.
 Reads with different length are supported.
 The k-mer counting part is substituted with KMC (http://sun.aei.polsl.pl/kmc).
@@ -52,7 +52,7 @@
 KMC is updated to 2.2.1 (The max memory usage of KMC can be fixed to 4 GB for any genome).
 A bug in writing a quality score hisgoram file is fixed.

-V1.00: 05/09/2015
+V1.00: 05/09/2015 (aka BLESS 2)
 Error correction algorithm is enhanced.
 Compressed input/output files are supported.
 Dependent libraries are included (Boost headers are still needed).

Home modified by Yun Heo

Yun Heo — Sun, 10 May 2015 10:17:28 -0000

--- v29
+++ v30
@@ -58,21 +58,25 @@
 Dependent libraries are included (Boost headers are still needed).
 Non-ACGTN characters can be handled.
 Non deterministic behaviors are corrected.
+
+V1.01: 05/10/2015
+Runtime is improved by 10%.
+All the dependent libraries are included.
+Errors in compiling pigz are fixed.
 



 #### System Requirements ####
-Compiling BLESS requires MPI libraries. The latest version was tested with GCC 4.9.2, MPICH 3.1.3
-(or OpenMPI 1.8.2).
+Compiling BLESS requires MPI libraries. The latest version of BLESS was tested
+with GCC 4.9.2, MPICH 3.1.3 (or OpenMPI 1.8.2).
 If you see the following error message, you need to upgrade your MPI library:
 error: initializing argument 2 of 'int MPI_File_open(MPI_Comm, char*, int, MPI_Info, ompi_file_t)'**
 



 #### Dependency ####
-Not included:
-Boost library (http://www.boost.org): static libraries are included; headers not included
 MPI: tested using MPICH 3.1.3 and OpenMPI 1.8.4

-Included:
+(Included dependent libraries)
+Boost library (http://www.boost.org)
 Google sparsehash (https://code.google.com/p/sparsehash)
 klib (https://github.com/attractivechaos/klib)
 KMC (http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about)

Home modified by Yun Heo

Yun Heo — Sat, 09 May 2015 06:12:14 -0000

--- v28
+++ v29
@@ -51,25 +51,39 @@
 V0.24: 01/29/2015
 KMC is updated to 2.2.1 (The max memory usage of KMC can be fixed to 4 GB for any genome).
 A bug in writing a quality score hisgoram file is fixed.
+
+V1.00: 05/09/2015
+Error correction algorithm is enhanced.
+Compressed input/output files are supported.
+Dependent libraries are included (Boost headers are still needed).
+Non-ACGTN characters can be handled.
+Non deterministic behaviors are corrected.
 



 #### System Requirements ####
-Compiling the program requires the BOOST C++ library (http://www.boost.org),
-the Google sparsehash library (https://code.google.com/p/sparsehash),
-and MPI libraries. The latest version was tested with GCC 4.7.1, MPICH 3.1.3
-(or OpenMPI 1.8.2), and BOOST 1.57.0.
+Compiling BLESS requires MPI libraries. The latest version was tested with GCC 4.9.2, MPICH 3.1.3
+(or OpenMPI 1.8.2).
 If you see the following error message, you need to upgrade your MPI library:
-
-**error: initializing argument 2 of 'int MPI_File_open(MPI_Comm, char*, int, MPI_Info, ompi_file_t**)'**
+error: initializing argument 2 of 'int MPI_File_open(MPI_Comm, char*, int, MPI_Info, ompi_file_t)'**
 



+#### Dependency ####
+Not included:
+Boost library (http://www.boost.org): static libraries are included; headers not included
+MPI: tested using MPICH 3.1.3 and OpenMPI 1.8.4
+
+Included:
+Google sparsehash (https://code.google.com/p/sparsehash)
+klib (https://github.com/attractivechaos/klib)
+KMC (http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about)
+murmurhash3 (https://code.google.com/p/smhasher)
+zlib (http://zlib.net)
+pigz (http://zlib.net/pigz)
+



 #### How to Install BLESS ####
-Specify your Boost include and library directories in Makefile
-using BOOST_INC and BOOST_LIB variables.
-Then type make.
+Type make.
 


-

 #### How to Run BLESS ####
 Single-end reads or merged paired-end reads

Home modified by Yun Heo

Yun Heo — Fri, 30 Jan 2015 03:13:50 -0000

--- v27
+++ v28
@@ -47,6 +47,10 @@

 V0.23: 12/19/2014
 Some bugs are fixed.
+
+V0.24: 01/29/2015
+KMC is updated to 2.2.1 (The max memory usage of KMC can be fixed to 4 GB for any genome).
+A bug in writing a quality score hisgoram file is fixed.
 



 #### System Requirements ####

Home modified by Yun Heo

Yun Heo — Sun, 11 Jan 2015 07:04:10 -0000

--- v26
+++ v27
@@ -86,8 +86,13 @@

 #### Parallelizing BLESS ####
-BLESS is parallelized using OpenMP and MPI. Consult your system admin about the MPI setting on your server.
-The number of threads per each node can be changed using "-smpthread" option (default: the number of cores in a SMP node).
+BLESS is parallelized using OpenMP and MPI. The number of threads per each node can be changed
+using "-smpthread" option (default: the number of cores in a SMP node).
+
+Using multiple nodes using MPI 
+Launch single process on a node and bind the processes to their nodes
+Ex) MPICH 3.1.3 Hydra Version
+> mpirun -ppn 1 -bind-to board ./bless -read1 <forward fastq> -read2 <reverse fastq> -prefix <output prefix> -kmerlength <k-mer length>

Home modified by Yun Heo

Yun Heo — Fri, 19 Dec 2014 20:52:47 -0000

--- v25
+++ v26
@@ -44,6 +44,9 @@

 V0.22: 12/17/2014
 MPI is applied to KMC.
+
+V0.23: 12/19/2014
+Some bugs are fixed.
 



 #### System Requirements ####