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Convert masked genome to N letters. $ perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna #Genome #Masked #N #Convert

fastq to fasta convertor $ sed -n '1~4s/^@/>/p;2~4p' test.fastq > test.fasta #Convert #Fasta #Fastq #fa #fq

MAF2Synteny https://github.com/fenderglass/maf2synteny #Convert #Synteny #MAF #Ragout

Convert MAF file format http://last.cbrc.jp/doc/maf-convert.html #MAF #Convert #Format

Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

MiraConvert http://manpages.ubuntu.com/manpages/xenial/man1/miraconvert.1.html #MIRA #Assembler #Convert