Requirements ============ linux machine (tested on debian testing and centos 7.3) at least 20Gb of RAM available for a plant genome ~500Mb the three binaries must be in your shell $PATH or copied into the $PG4CBIN directory (see below) minimap2 (https://github.com/lh3/minimap2) bedtools (https://github.com/arq5x/bedtools2/releases) blastn (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) perl >= 5.10 Install ======= gzip -cd PrepareGaps4Circos-20180716.tar.gz | tar xvf - sh|bash: export PG4CBIN $PWD/PrepareGaps4Circos-20180719/bin csh|tcsh: setenv PG4CBIN $PWD/PrepareGaps4Circos-20180719/bin Warning: the scope of this setting is your current session. You must add it to your shell configuration file (with a full path) to use it accross sessions. Run === create a directory and copy the raw assemblies (fasta files) into it (e.g: mkdir assembliesdir && cp /...../myably1.fa /...../myably2.fa assembliesdir) $PG4CBIN/lipm_prepare_gaps_4circos.pl --assembliesdir $PWD/assembliesdir --genome mygenome.fasta --circosdir mycircosdir If everything runs well: - the file mycircosdir/circos.conf contains a valid configuration file for circos (http://circos.ca). Note that you may need to edit/adapt the <