1220 days ago
Set up WGD environment using conda !
...py) ... done Created wheel for wgd: filename=wgd-1.2-py3-none-any.whl size=75291 sha256=56a7a19b3f4e5358.... done Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689200 sha256=7daa115fd1b05...1216 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...Writer.cpp:24:8: warning: ‘%x’ directive writing 1 byte into a region of size between 0 and 6 [-Wformat-ove...iltin___sprintf_chk’ output between 8 and 26 bytes into a destination of size 8 __bos (__s), __fmt,...1216 days ago
Commandline for paired end reads simulation with BBMap !
...len=(0-0) genome=1 PERFECT_READ_RATIO=0.0 ADD_ERRORS_FROM_QUALITY=true REPLACE_NOREF=false paired=true read length=250 reads=100000 insert size=400-600 Wrote reads_BBMAP250...1002 days ago
Tadpole is 250x faster than SPADes assembler !
...or lower. prehashes=2 Number of hashes for prefilter. prefiltersize=0.2 (pff) Fraction of memor...h. Trimming by K/2 may yield more accurate genome size estimation. contigpasses=16...988 days ago
963 days ago
Bash script to simulate a genome !
...indelrate=0.001 \ maxindel=20 \ nohomopolymers=t \ hetrate=1 2> GCA_003401745.1_ASM340174v1_genomic.fna_upper.diploid.fasta.log.txt # genome size bgzip -@75 -cd GCA_003401745...930 days ago
Bash script to split multifasta file !
...n easily split a file (multi.fa) into chunks of size N (here, N=500), by using the...nt >> file; }' < multi.fa #OR awk -v chunksize=$(grep ">" multi.fasta -c) 'B...chunksize=int(chunksize/10)+1 } /^>/ {if(n%chunksize==0){file=sprintf("chunk%d.fa"...836 days ago
312 days ago