Biobambam2
- bam12auxmerge(1) bam12auxmerge - merge two BAM files
- bam12split(1) bam12split - project rank pairs produced by bamcollate2 to single ranks per read
- bam12strip(1) bam12strip - remove rank left by bam12split from read names
- bamadapterclip(1) bamadapterclip - remove the adapters marked by bamadapterfind
- bamadapterfind(1) bamadapterfind - find adapter contamination in sequencing reads
- bamalignfrac(1) compute fraction of aligned bases in alignment file
- bamauxmerge(1) bamauxmerge - merge information in unmapped and mapped alignment files
- bamauxmerge2(1) bamauxmerge2 - merge information in unmapped and mapped BAM files
- bamauxsort(1) bamauxsort - filter auxiliary tags from BAM file
- bambisect(1) bambisect - find reduced size BAM file on which a program fails
- bamcat(1) bamcat - concatenate BAM files
- bamchecksort(1) bamchecksort - check sort order of a BAM file
- bamclipreinsert(1) bamclipreinsert - reinsert query sequence fragments removed by bamadapterclip
- bamclipXT(1) bamclipXT - reinsert query sequence fragments removed by bamadapterclip
- bamcollate2(1) bamcollate2 - collate reads in a SAM, BAM or CRAM file by name
- bamconsensus(1) bamconsensus - compute rough consensus sequence from alignments
- bamdownsamplerandom(1) bamdownsamplerandom - downsample a SAM, BAM or CRAM file
- bamfeaturecount(1) bamfeaturecount - evaluate alignments produce by an RNA-seq aligner
- bamfillquery(1) bamfillquery - fill query sequences into BAM files
- bamfilteraux(1) bamfilteraux - filter auxiliary tags from BAM file
- bamfilterflags(1) bamfilterflags - remove entries from BAM files matching a given set of flags
- bamfilterheader(1) bamfilterheader - filter auxiliary tags from BAM file
- bamfilterheader2(1) bamfilterheader2 - filter auxiliary tags from BAM file
- bamfiltermc(1) bamfiltermc - remove MC aux fields for reads with unmapped mates
- bamfilterrg(1) bamfilterrg - filter read groups from a BAM file
- bamfixmateinformation(1) bamfixmateinformation - fix mate pair information in BAM files
- bamflagsplit(1) bamflagsplit - sort BAM files by coordinate or query name
- bamindex(1) bamindex - create index for BAM file
- bamintervalcomment(1) bamintervalcomment - sort BAM files by coordinate or query name
- bammarkduplicates(1) bammarkduplicates - mark duplicate reads/alignments in BAM files
- bammarkduplicates2(1) bammarkduplicates2 - mark duplicate reads/alignments in BAM files
- bammarkduplicatesopt(1) bammarkduplicatesopt - mark duplicate reads/alignments in BAM files
- bammaskflags(1) remove flags from alignments
- bammdnm(1) bammdnm - compute MD and NM fields
- bammerge(1) bammerge - merge BAM files
- bamrank(1) bamrank - insert the rank (line number) of each alignment as an auxiliary field for tag zz
- bamranksort(1) bamranksort - sort BAM files by rank
- bamrecalculatecigar(1) bamrecalculatecigar - concatenate BAM files
- bamrecompress(1) bamrecompress - recompress BAM file
- bamreset(1) bamreset - reset BAM file to unaligned state
- bamseqchksum(1) bamseqchksum - produce checksums for primary data in BAM files
- bamsormadup(1) bamsormadup - sort name collated SAM or BAM file by coordinate and mark duplicates or sort SAM or BAM file by query name
- bamsort(1) bamsort - sort BAM files by coordinate or query name
- bamsplit(1) bamsplit - split BAM files
- bamsplitdiv(1) bamsplitdiv - split BAM file into a set of BAM files
- bamstreamingmarkduplicates(1) bamstreamingmarkduplicates - mark duplicate reads
- bamtagconversion(1) bamtagconversion - convert old tags to new ones
- bamtofastq(1) bamtofastq - convert SAM, BAM or CRAM files to FastQ
- bamvalidate(1) bamvalidate - validate BAM file
- bamzztoname(1) bamzztoname - move the rank of an alignment stored as an auxiliary field to the alignments name
- fastaexplod(1) fastaexplod - split multi sequence FastA file into one file per sequence
- fastqtobam(1) fastqtobam - convert FastQ to unmapped BAM
- filtergtf(1) filtergtf - filter a gtf annotation file for use with bamfeaturecount
- normalisefasta(1) normalisefasta - normalise line length in a FastA file