Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1297 days ago
1229 days ago
1229 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
...read.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Fai...ome/urbe/anaconda3/envs/wgd/./testset -- Installing: /home/urbe...ome/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210...ome/urbe/anaconda3/envs/wgd/./testset/datasetII/ptr_lists_030210...1217 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq...h=250, mininsert=400, maxinsert=600, gaussian] Writing reference. Executing dna....1003 days ago
Tadpole is 250x faster than SPADes assembler !
lege@jit-Lenovo-ideapad-320-15ISK:~/Downlo...(bm1) Min ratio of 1st to 2nd-greatest path depth at high depth. br...(bm2) Min ratio of 1st to 2nd-greatest path depth at low depth. bra...via overlap, but do not merge reads. testmerge=t Test kmer coun...989 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$t...$text" | sed 's/ \$//g' #Multiple space cat /tmp/test.txt | sed 's/[ ]\+/ /g' ec...xt1" | awk '{ gsub(/[ ]+/," "); print }' cat /tmp/test.txt | awk '{ gsub(/[ ]+/," ")...969 days ago
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942 days ago
Bash script to simulate a genome !
# Reference https://github.com/chhylp123/h...r PacBio assembly cd /genetics/elbers/test/fly2 wget https://ftp.ncbi.n...bx.psu.edu/ mkdir -p /genetics/elbers/test/fly2/kmergenie-illumina-raw-r...p maximum 30000bp cd /genetics/elbers/test/fly2 /genetics/elbers/bbma...931 days ago