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cmonjeau/masurca

By cmonjeau

•Updated about 8 years ago

MaSuRCA Genome Assembler

Image
0

176

cmonjeau/masurca repository overview

⁠TO BUILD

docker build -t sauloal/masurca .

⁠TO RUN MANUALLY :

⁠FROM INSIDE THE FOLDER CONTAINING THE MOUSE DATA, RUN:

chmod o+w . docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca bash masurca mm_config.cfg ./assembly.sh

⁠TO RUN AUTOMATICALLY

⁠FROM INSIDE THE FOLDER CONTAINING THE MOUSE DATA, RUN:

chmod o+w . docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca masurca mm_config.cfg docker run --rm -it --name masurca_mouse -v $PWD:/data:rw sauloal/masurca ./assembly.sh

⁠Example configuration file

⁠mm_config.cfg

DATA

PE= pe 180 20 /data/pe_1.fastq /data/pe_2.fastq

JUMP= j1 1834 182 /data/sj_1834_182_1.fastq /data/sj_1834_182_2.fastq

JUMP= j2 2289 2794 /data/sj_2289_212_1.fastq /data/sj_2289_212_2.fastq

JUMP= j3 2794 220 /data/sj_2794_220_1.fastq /data/sj_2794_220_2.fastq

JUMP= j4 -38453 3557 /data/lj_38453_3557_2.fastq /data/lj_38453_3557_1.fastq

END

GRAPH_KMER_SIZE=auto

USE_LINKING_MATES=0

LIMIT_JUMP_COVERAGE = 60

CA_PARAMETERS = ovlMerSize=30 cgwErrorRate=0.10 ovlMemory=40GB

KMER_COUNT_THRESHOLD = 1

NUM_THREADS= 20

JF_SIZE=10000000000

DO_HOMOPOLYMER_TRIM=0

END

Tag summary

Content type

Image

Digest

Size

530 MB

Last updated

about 8 years ago

docker pull cmonjeau/masurca:3.2.8