yaraYara is an exact tool for aligning DNA sequencing reads to reference genomes.http://www.seqan.de/yara/yarabiotools:yara0.9.6Command-line toolhttp://edamontology.org/topic_0102MappingLinuxWindowsMacC++http://edamontology.org/operation_3198Read mappinghttps://docker-ui.genouest.org/app/#/container/bioconda/yaraContainer filehttps://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/yara_indexer.cwlTool wrapper (CWL)https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/yara_mapper.cwlTool wrapper (CWL)https://anaconda.org/bioconda/yaraContainer filehttp://www.seqan.de/apps/yara/General10.1093/nar/gkt00523358824PMC3627565Enrico Siragusaenrico.siragusa@fu-berlin.dehttp://www.seqan.de/contact/PersonPrimary contactBWAFast, 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/0000-0003-4874-2874PersonContributorBowtie 2Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.http://bowtie-bio.sourceforge.net/bowtie2/index.shtmlbowtie2biotools:bowtie2RRID:SCR_016368rridCommand-line toolhttp://edamontology.org/topic_0102Mappinghttp://edamontology.org/topic_0622Genomicshttp://edamontology.org/topic_0102MappingLinuxC++GPL-3.0galaxyPasteurMatureOpen accesshttp://edamontology.org/operation_3198Read mappinghttp://edamontology.org/data_2977Nucleic acid sequencehttp://edamontology.org/format_1930FASTQ

http://edamontology.org/data_1383Sequence alignment (nucleic acid)http://edamontology.org/format_2572BAMhttp://edamontology.org/format_2573SAM

https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/bowtie2/bowtie2/2.2.6.2Galaxy servicehttps://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bowtie2.cwlTool wrapper (CWL)https://gitlab.com/sibyllewohlgemuth/cwl_files/raw/master/bowtie2_build.cwlTool wrapper (CWL)https://docker-ui.genouest.org/app/#/container/bioconda/bowtie2Container filehttps://anaconda.org/bioconda/bowtie2Container filehttps://tracker.debian.org/pkg/bowtie2Software packageLink to the Debian package information. This form of the link is recommended by the Debian devs & Med team, and in the future all this information, including versions, will be pushed to GitHub automatically (matuskalas)2.2.4-1, 2.3.0-2, 2.3.4.3-1, 2.3.5.1-1, 2.3.5.1-1https://bioconda.github.io/recipes/bowtie2/README.htmlSoftware packageLink to the Bioconda package information. This form of the link is recommended by the Bioconda team, and in the future all this information, including versions (limit 100 chars), will be pushed to GitHub automatically (matuskalas)2.3.5-0, 2.3.4.3-1 - 2.3.0-0, 2.2.8-2 - 2.2.1-0http://bowtie-bio.sourceforge.net/bowtie2/manual.shtmlUser manualhttps://github.com/BenLangmead/bowtie2General10.1038/nmeth.192322388286PMC3322381Primary10.1186/1471-2105-14-18423758764PMC3694458Benchmarking study10.1016/j.ygeno.2017.03.00128286147Other10.1186/1471-2164-15-26424708189PMC4051166Benchmarking study10.1093/bioinformatics/btu14624626854Other10.7490/f1000research.1114334.1OtherInstitut Français de BioinformatiqueInstituteProviderBen Langmeadhttp://bowtie-bio.sourceforge.net/bowtie2/index.shtmlDeveloperBen Langmeadhttp://bowtie-bio.sourceforge.net/bowtie2/index.shtmlPersonPrimary contact