Tools for bacterial whole genome annotation
...MAKER Web Annotation Service (MWAS). MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains t...2326 days ago
Run miniasm assembler on nanopore reads !
...tq ONT_A.fasta minimap2 -xava-ont ONT_A.fasta ONT_A.fasta -t10 -X > AONT.paf awk '{if($1==$6){print}}' AONT.paf > A...00final.eps minidot -f 5 -m 10000 AONTself.paf > AONTself10000.eps sed 's/_template...2324 days ago
BBSplit: Read Binning Tool for Metagenomes and Contaminated Libraries
...input file is paired and interleaved. For single-end reads you would leave that out. For paired reads in 2 files, you would do this:bbsplit.sh in1=reads1.fq in2=reads2.fq ref=ecoli.fa...2309 days ago
2299 days ago
PerlOneLiner for Bioinformatician
...d a file so that every set of 10 lines becomes one tab-separated lineperl -lpe '$\ = $. % 10 ? "\t" : "\n"' LINE NUMBERI...number is a primeperl -lne '(1x$_) !~ /^1?$|^(11+?)\1+$/ &am...scii)'perl -le '@ascii = (99, 111, 100, 105, 110, 103); print...2296 days ago
List of visualization tools for network biology
.../sites.google.com/site/medusa3visualization/ NAViGaTOR Visualizing and analyzing protein-protein interaction networks http://tinyurl.com/navigator1/ N-Browse Interactive graph...2282 days ago
List of visualization tools for genome alignments
...otator.htm JVM Java Visual Mapping tool for NGS reads http://www.springer.com/cda/content/document/cda_downloaddocument/9789401792448-c2.pdf?SGWID=0-0-45-1487072-p176815501 LookSeq&nbs...2278 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
...sh; remove directory dir recursively cp file1 file2 — copy file1 to file2 cp -r dir1 dir2 ...and execute only 2 — write only 1 — execute only 0&n...line alt+f — move cursor forward 1 word alt+b — move...2275 days ago
Awk for Bioinformatician and computational biologist
...The basic syntax is: awk '/pattern1/ {Actions} /pattern2/ {Action...contents: $ cat data/test.tsvcontig1 ACTGTCTGTCACTGTGTTGTGATGTTGTG...e has 5 words, it will be stored in $1, $2, $3, $4 and $5. $0 repres...5 ACTTTATATATT<=14We can also use 1 after the last block {} to pr...2274 days ago
Computational resources for TE discovery and TE detection
.../retrolab/data/LTR_Struc.html LTR_MINER http://genomebiology.com/2004/5/10/R79/suppl/s7 LTR_par http:.../trf/trf.html Transposon Cluster Finder http://www.mssm.edu/labs/warbup01/paper/files.html TE nest ht...2268 days ago