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