BWAFast, accurate, memory-efficient aligner for short and long sequencing readshttp://bio-bwa.sourceforge.netbwabiotools:bwaCommand-line toolWorkbenchhttp://edamontology.org/topic_0102MappingLinuxMacCMITBWAMaturehttp://edamontology.org/operation_3211Genome indexinghttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTA

http://edamontology.org/data_3210Genome index

Index database sequences in the FASTA format. databasehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_3210Genome indexhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_1916Alignment

Align 70bp-1Mbp query sequences with the BWA-MEM algorithm. Briefly, the algorithm works by seeding alignments with maximal exact matches (MEMs) and then extending seeds with the affine-gap Smith-Waterman algorithm (SW). The BWA-MEM algorithm performs local alignment. It may produce multiple primary alignments for different part of a query sequence. This is a crucial feature for long sequences. However, some tools such as Picards markDuplicates does not work with split alignments. One may consider to use option -M to flag shorter split hits as secondary.http://edamontology.org/operation_3198Read mappinghttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1332FASTA search results formathttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_2012Sequence coordinates

Find the SA coordinates of the input reads. reference sequence query sequencehttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQhttp://edamontology.org/data_2044Sequence

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAM

Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen reference sequence query sequencehttp://edamontology.org/operation_3429Generationhttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_0863Sequence alignmenthttp://edamontology.org/format_2573SAM

Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly. reference sequencehttp://edamontology.org/operation_0292Sequence alignmenthttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1929FASTAhttp://edamontology.org/data_2044Sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_0863Sequence alignment

Align query sequences in the in.fq file reference sequencehttps://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_index.cwlTool wrapper (CWL)https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bwa_mem.cwlTool wrapper (CWL)https://docker-ui.genouest.org/app/#/container/bioconda/bwaContainer filehttps://anaconda.org/bioconda/bwaContainer filehttp://bio-bwa.sourceforge.net/bwa.shtmlUser manual10.1093/bioinformatics/btp32419451168PMC2705234Primary10.1186/1471-2105-14-18423758764PMC3694458Benchmarking study10.1016/j.ygeno.2017.03.0012828614710.1186/1471-2164-15-26424708189PMC4051166Benchmarking study10.1093/bioinformatics/btu1462462685410.1093/bioinformatics/btp69820080505PMC2828108bwa teambio-bwa-help@sourceforge.netPersonPrimary contactHeng Lime@liheng.orghttp://www.liheng.org/http://orcid.org/0000-0003-4874-2874PersonContributor