Large-scale gene sequence lossless parallel compression method based on Spark

Large-scale gene sequence lossless parallel compression method based on Spark

The invention discloses a large-scale gene sequence lossless parallel compression method based on Spark, which comprises the following steps of: preprocessing a reference sequence and a sequence to be compressed: extracting a basic base sequence of the reference sequence and constructing a matching...

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Hauptverfasser: FANG HOUZHI, JI YIMU, YAO HAICHANG, HU GUANGYONG, PENG JIANHUA, ZHANG YIFAN
Format: Patent
Sprache:chi ; eng
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INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
PHYSICS
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creator FANG HOUZHI
JI YIMU
YAO HAICHANG
HU GUANGYONG
PENG JIANHUA
ZHANG YIFAN
description The invention discloses a large-scale gene sequence lossless parallel compression method based on Spark, which comprises the following steps of: preprocessing a reference sequence and a sequence to be compressed: extracting a basic base sequence of the reference sequence and constructing a matching index by a main node; sending the basic base sequence of the reference sequence and the matching index of the basic base sequence to all working nodes in the form of compressed broadcast variables; each working node extracts a basic base sequence of a sequence to be compressed in parallel and creates RDD, and sequence auxiliary information is independently coded and stored; and finally obtaining a compressed file through a first parallel matching step, a second matching index construction step and a second parallel matching step. According to the method, large-scale gene secondary iteration compression and the characteristics of Spark based on a memory distribution data set are fully combined, and compared with oth
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subjects INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTEDFOR SPECIFIC APPLICATION FIELDS
PHYSICS
title Large-scale gene sequence lossless parallel compression method based on Spark
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