Section 1 of the manual describes user commands and tools, for example, file manipulation tools, shells, compilers, web browsers, file and image viewers and editors, and so on.
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- bacula-tray-monitor
- Bacula's 'System Tray' monitor
- balboa-backend-console
- Backend maintenance console for balboa
- balboa-bench
- Run a number of queries against given endpoint
- balboa-help
- Help about any command
- balboa-makeman
- Create man pages
- balboa-mock
- Mock backend
- balboa-query
- Obtain information from pDNS about IP ranges
- balboa-rocksdb
- RocksDB backend for balboa
- balboa-serve
- Run the balboa frontend
- balboa
- BAsic Little Book Of Answers
- bali-phy-pkg
- Manage BAli-Phy packages
- bali-phy
- Bayesian Inference of Alignment and Phylogeny
- bali-subsample
- subsample - Subsample lines in a file
- balls
- preprocessor for space-filling models in Raster3D molecular graphics package
- ballview
- BALLView - A free molecular modeling and molecular graphics tool
- balsa-ab
- Balsa - the GNOME e-mail client
- balsa
- Balsa - the GNOME e-mail client
- bam-read
- Parse bam files after multi-mapping reads have been assigned and aggregate read mapping information by contig
- bam
- fast and flexible build system
- bam12auxmerge
- merge two BAM files
- bam12split
- project rank pairs produced by bamcollate2 to single ranks per read
- bam12strip
- remove rank left by bam12split from read names
- bam2bed
- manual page for bam2bed 2.4.41+dfsg
- bam2hints
- convert mRNA-to-genome alignments in BAM format into a hint file for AUGUSTUS
- bam2starch
- manual page for bam2starch 2.4.41+dfsg
- bam2wig
- Convert bam files to wiggle files. Can be used to generate exonpart hints for AUGUSTUS
- bam_pipeline
- BAM pipeline of PALEOMIX suite
- bam_rmdup_collapsed
- filter BAM file for PCR duplicates
- bamadapterclip
- remove the adapters marked by bamadapterfind
- bamadapterfind
- find adapter contamination in sequencing reads
- bamalignfrac
- compute fraction of aligned bases in alignment file
- bamauxmerge
- merge information in unmapped and mapped alignment files
- bamauxmerge2
- merge information in unmapped and mapped BAM files
- bamauxsort
- filter auxiliary tags from BAM file
- bambisect
- find reduced size BAM file on which a program fails
- bamcat
- concatenate BAM files
- bamchecksort
- check sort order of a BAM file
- bamcleanheader.py
- remove illegal and malformed fields from a BAM file's header
- bamclipXT
- reinsert query sequence fragments removed by bamadapterclip
- bamclipreinsert
- reinsert query sequence fragments removed by bamadapterclip
- bamcollate2
- collate reads in a SAM, BAM or CRAM file by name
- bamconsensus
- compute rough consensus sequence from alignments
- bamdownsamplerandom
- downsample a SAM, BAM or CRAM file
- bamfeaturecount
- evaluate alignments produce by an RNA-seq aligner
- bamfillquery
- fill query sequences into BAM files
- bamfilteraux
- filter auxiliary tags from BAM file
- bamfilterflags
- remove entries from BAM files matching a given set of flags
- bamfilterheader
- filter auxiliary tags from BAM file
- bamfilterheader2
- filter auxiliary tags from BAM file
- bamfiltermc
- remove MC aux fields for reads with unmapped mates
- bamfilterrg
- filter read groups from a BAM file
- bamfilterrg.py
- filter readgroup(s) from a BAM file
- bamfixflags.py
- filter readgroup(s) from a BAM file
- bamfixmateinformation
- fix mate pair information in BAM files
- bamflagsplit
- sort BAM files by coordinate or query name
- bamg
- bidimensional anisotropic mesh generator (rheolef-7.2)
- bamg2geo
- convert bamg mesh in geo format (rheolef-7.2)
- bamgroupreads.py
- Group BAM file by read IDs without sorting
- bamheadrg.py
- Inject readgroup info
- bamindex
- create index for BAM file
- bamintervalcomment
- sort BAM files by coordinate or query name
- bamlibs.py
- output comma delimited string of read group IDs for each library
- bammarkduplicates
- mark duplicate reads/alignments in BAM files
- bammarkduplicates2
- mark duplicate reads/alignments in BAM files
- bammarkduplicatesopt
- mark duplicate reads/alignments in BAM files
- bammaskflags
- remove flags from alignments
- bammdnm
- compute MD and NM fields
- bammerge
- merge BAM files
- bamrank
- insert the rank (line number) of each alignment as an auxiliary field for tag zz
- bamranksort
- sort BAM files by rank
- bamrecalculatecigar
- concatenate BAM files
- bamrecompress
- recompress BAM file
- bamreset
- reset BAM file to unaligned state
- bamseqchksum
- produce checksums for primary data in BAM files
- bamsormadup
- sort name collated SAM or BAM file by coordinate and mark duplicates or sort SAM or BAM file by query name
- bamsort
- sort BAM files by coordinate or query name
- bamsplit
- split BAM files
- bamsplitdiv
- split BAM file into a set of BAM files
- bamstreamingmarkduplicates
- mark duplicate reads
- bamtagconversion
- convert old tags to new ones
- bamtofastq
- convert SAM, BAM or CRAM files to FastQ
- bamtofastq.py
- Convert a coordinate sorted BAM file to FASTQ
- bamtools
- toolkit for manipulating BAM (genome alignment) files
- bamvalidate
- validate BAM file
- bamview
- visualizing genome sequencing read alignment stored in BAM files
- bamzztoname
- move the rank of an alignment stored as an auxiliary field to the alignments name
- banana
- Plot bending and curvature data for B-DNA
- bandit
- Security oriented static analyzer for python code
- banner
- print large banner
- baobab
- A graphical disk usage analyzer for the GNOME desktop
- bar
- show information about a data transfer
- barcode
- a standalone program to convert text strings to printed bars
- bardecode
- barcode recognition tool of the ExactImage toolkit
- barebox-state
- Manage Barebox's state in a device tree
- barectf
- Generate C99 code that can write native CTF packets
- baresip
- portable and modular command-line SIP user-agent
- bargraph
- compile bar graphs into pic input
- barman-cloud-backup-delete
- Delete backups stored in the Cloud
- barman-cloud-backup-keep
- Flag backups which should be kept forever
- barman-cloud-backup-list
- List backups stored in the Cloud