{"id":6200,"date":"2012-03-27T10:10:04","date_gmt":"2012-03-27T08:10:04","guid":{"rendered":"http:\/\/www.ehu.es\/sgi\/?p=6200"},"modified":"2012-06-21T01:17:07","modified_gmt":"2012-06-20T23:17:07","slug":"abyss-3","status":"publish","type":"post","link":"https:\/\/www.ehu.eus\/sgi\/scientific-software\/abyss-3","title":{"rendered":"ABySS"},"content":{"rendered":"

General Information<\/h2>\n

1.3.2 version of ABySS (A<\/strong>ssembly By S<\/strong>hort S<\/strong>equences). ABySS is a de novo<\/em>, parallel, paired-end sequence assembler that is designed for short reads. ABySS can be executed in parallel.<\/p>\n

See also the installed [intlink id=\u00bb6043″ type=\u00bbpost\u00bb]velvet[\/intlink] and comparing both we have published article<\/a>.<\/p>\n

How to use<\/h2>\n

The executables can be found in \/software\/abyss\/bin<\/code>. To run abyss in a script type in it:<\/p>\n

\/software\/abyss\/bin\/abyss-pe [abyss-pe options]<\/pre>\n
Performance<\/h2>\n
See also the installed [intlink id=\u00bb6043″ type=\u00bbpost\u00bb]velvet[\/intlink] and comparing both we have published article<\/a>.<\/p>\n
Parallelization<\/h3>\n
Some benchmarks has been performed with ABySS. They have been performed using file from an Illumina HiSeq2000 NGS with 100 bp per sequence. In the table 1 we can see an example about how ABySS scales as a function of the number of cores. As we can see ABySS scales very up to 8 cores. The results is valid unless for more than 10e6 sequences.<\/p>\n\n\n\n\n\n\n
Table 1. Execution time of abyss-pe<\/code> in seconds as a function the number of cores<\/caption>\n
cores<\/strong><\/td>\n2<\/td>\n4<\/td>\n8<\/td>\n12<\/td>\n24<\/td>\n<\/tr>\n
Time (s)<\/td>\n47798<\/td>\n27852<\/td>\n16874<\/td>\n14591<\/td>\n18633<\/td>\n<\/tr>\n
Aceleration<\/td>\n1<\/td>\n1.7<\/td>\n2.8<\/td>\n3.3<\/td>\n2.6<\/td>\n<\/tr>\n
Performance(%)<\/td>\n100<\/td>\n86<\/td>\n71<\/td>\n55<\/td>\n21<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
Execution time<\/h3>\n
We have analized as well the execution time as a function of the size of the data. In the table 2 we\u00a0 observe how from 1 million to 10 millions of sequences the execution time increases by 10 as well. From 10 to 100 millions of sequences the time increases a little more, between 10 t0 20. Therefore, the behavior is more or less lineal.<\/p>\n\n\n\n\n\n\n
Table 2. Execution time in seconds of abyss-pe<\/code> executed in 2, 4 y 8 cores as a function of the number of processed sequences.<\/caption>\n
sequences<\/strong><\/td>\n10e6<\/td>\n10e7<\/td>\n10e8<\/td>\n<\/tr>\n
Time in 2 cores (s)<\/td>\n247<\/td>\n2620<\/td>\n47798<\/td>\n<\/tr>\n
Time in 4 cores (s)<\/td>\n134<\/td>\n1437<\/td>\n27852<\/td>\n<\/tr>\n
Time in 8 cores (s)<\/td>\n103<\/td>\n923<\/td>\n16874<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
RAM memory<\/h3>\n
In these kind of programs more important than the execution time, which is reasonable, is the RAM memory usage, which can limit the calculation type. In the table 3 we observe how the RAM increases as a function of the number of sequences. We also show the logarithms of the measured values which has been used for a lineal regression. The jobs has been performed in 12 cores.<\/p>\n\n\n\n\n\n\n
Tabl3 3. RAM memory used by abyss-pe<\/code> as a function of the number of processed sequences. The logarithms of the measured values are also shown.<\/caption>\n
sequences<\/strong><\/td>\n10e6<\/td>\n5*10e6<\/td>\n10e7<\/td>\n5*10e7<\/td>\n10e8<\/td>\n<\/tr>\n
RAM (GB)<\/td>\n4.0<\/td>\n7.6<\/td>\n11<\/td>\n29<\/td>\n44<\/td>\n<\/tr>\n
log(sequences)<\/td>\n6<\/td>\n6.7<\/td>\n7<\/td>\n7.7<\/td>\n8<\/td>\n<\/tr>\n
log(RAM)<\/td>\n0.60<\/td>\n0.88<\/td>\n1.03<\/td>\n1.46<\/td>\n1.65<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
From the values of the table we obtain a fitting of the RAM in GB as a function of the number of sequences (s<\/em>) to the equation<\/p>\n
log(RAM)=0.53*log(s)-2.65<\/p>\n
o equivalently<\/p>\n
RAM=(s^0.53)\/447<\/p>\n
Conclusion<\/h3>\n
The memory usage is smaller than in other assemblers like [intlink id=\u00bb6043″ type=\u00bbpost\u00bb]Velvet[\/intlink], see as well the report Velvet performance in the machines of the Computing Service of the UPV\/EHU<\/em><\/a><\/em> and comparing both we have published article<\/a>. In addition, the parallelization with MPI of ABySS allows to aggregate the RAM memory of several nodes to perform larger calculations.<\/p>\n
More information<\/h2>\n
ABySS<\/a> web page.
\n[intlink id=\u00bb6043″ type=\u00bbpost\u00bb]Velvet[\/intlink] assembler.
\nVelvet performance in the machines of the Computing Service of the UPV\/EHU<\/em><\/a> report.<\/p>\n
Velvet and ABySS performance in the machines of the Computing Service of the UPV\/EHU<\/a>, post in the hpc blog<\/a>.<\/p>\n
abyss-pe<\/code><\/div>\n","protected":false},"excerpt":{"rendered":"
General Information 1.3.2 version of ABySS (Assembly By Short Sequences). ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS can be executed in parallel. See also the installed [intlink id=\u00bb6043″ type=\u00bbpost\u00bb]velvet[\/intlink] and comparing both we have published article. How to use The executables can be found in \/software\/abyss\/bin. … Seguir leyendo ABySS<\/span> →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_links_to":"","_links_to_target":""},"categories":[239,196],"tags":[],"_links":{"self":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6200"}],"collection":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/comments?post=6200"}],"version-history":[{"count":14,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6200\/revisions"}],"predecessor-version":[{"id":6457,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/posts\/6200\/revisions\/6457"}],"wp:attachment":[{"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/media?parent=6200"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/categories?post=6200"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ehu.eus\/sgi\/wp-json\/wp\/v2\/tags?post=6200"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}