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‎records/abacas.json

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processing /home/moeller/git/debian-med/abacas...

‎records/abyss.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "ABySS",
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"collection": "DebianMed",
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"version": "2.0.2-2",
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"publications": {
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"publicationsPrimaryID": [
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"10.1101/gr.089532.108"
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]
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},
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"homepage": "http://www.bcgsc.ca/platform/bioinfo/software/abyss",
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"description": "de novo, parallel, sequence assembler for short reads\n ABySS is a de novo, parallel, sequence assembler that is designed for\n short reads. It may be used to assemble genome or transcriptome\n sequence data. Parallelization is achieved using MPI, OpenMP and\n pthread."
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}

‎records/adapterremoval.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "AdapterRemoval",
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"collection": "DebianMed",
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"version": "2.2.0-1",
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"publications": {
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"publicationsPrimaryID": [
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"10.1186/s13104-016-1900-2"
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]
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},
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"homepage": "https://github.com/MikkelSchubert/adapterremoval",
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"description": "rapid adapter trimming, identification, and read merging of gene sequences\n This program searches for and removes remnant adapter sequences from High-\n Throughput Sequencing (HTS) data and (optionally) trims low quality\n bases from the 3' end of reads following adapter removal. AdapterRemoval\n can analyze both single end and paired end data, and can be used to\n merge overlapping paired-ended reads into (longer) consensus sequences.\n Additionally, the AdapterRemoval may be used to recover a consensus\n adapter sequence for paired-ended data, for which this information is\n not available."
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}

‎records/aegean.json

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{
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"function": [
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{
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"input": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_1255"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1975"
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}
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]
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}
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],
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"functionHandle": "summary",
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"functionName": [
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{
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"uri": "http://edamontology.org/operation_3194"
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},
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{
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"uri": "http://edamontology.org/operation_2121"
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}
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],
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"output": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_1255"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1975"
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}
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]
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},
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2048"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_2330"
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}
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]
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}
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]
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}
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],
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"sourceRegistry": "",
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"name": "aegean",
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"collection": "DebianMed",
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"topic": [
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{
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"uri": "http://edamontology.org/topic_3168"
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}
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],
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"version": "0.15.2+dfsg-1",
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"publications": {
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"publicationsPrimaryID": [
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"10.1186/1471-2105-13-187"
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]
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},
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"homepage": "http://standage.github.io/AEGeAn",
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"description": "integrated genome analysis toolkit\n The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome\n Annotations. The toolkit includes a variety of analysis programs, e.g. for\n comparing distinct sets of gene structure annotations (ParsEval), computation\n of gene loci (LocusPocus) and more."
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}

‎records/alter-sequence-alignment.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "ALTER",
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"collection": "DebianMed",
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"version": "1.3.3+dfsg-1",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/nar/gkq321"
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]
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},
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"homepage": "http://sing.ei.uvigo.es/ALTER/",
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"description": "genomic sequences ALignment Transformation EnviRonment\n ALTER (ALignment Transformation EnviRonment) is a tool to transform\n between multiple sequence alignment formats. ALTER focuses on the\n specifications of mainstream alignment and analysis programs rather than\n on the conversion among more or less specific formats."
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}

‎records/altree.json

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processing /home/moeller/git/debian-med/altree...

‎records/amap-align.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "amap-align",
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"collection": "DebianMed",
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"version": "2.2-7",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/bioinformatics/btl311"
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]
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},
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"homepage": "http://code.google.com/p/amap-align/",
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"description": "Protein multiple alignment by sequence annealing\n AMAP is a command line tool to perform multiple alignment of peptidic\n sequences. It utilizes posterior decoding, and a sequence-annealing\n alignment, instead of the traditional progressive alignment method. It is\n the only alignment program that allows one to control the sensitivity /\n specificity tradeoff. It is based on the ProbCons source code, but\n uses alignment metric accuracy and eliminates the consistency\n transformation.\n .\n The java visualisation tool of AMAP 2.2 is not yet packaged in Debian."
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}

‎records/andi.json

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{
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"function": [
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{
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"input": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2044"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1929"
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}
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]
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}
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],
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"functionHandle": "summary",
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"functionName": [
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{
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"uri": "http://edamontology.org/operation_0289"
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}
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],
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"output": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_0870"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1423"
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}
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]
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}
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]
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}
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],
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"sourceRegistry": "",
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"name": "andi",
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"collection": "DebianMed",
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"topic": [
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{
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"uri": "http://edamontology.org/topic_3293"
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}
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],
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"version": "0.10-3",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/bioinformatics/btu815"
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]
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},
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"homepage": "https://github.com/EvolBioInf/andi",
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"description": "Efficient Estimation of Evolutionary Distances\n This is the andi program for estimating the evolutionary distance \n between closely related genomes. These distances can be used to rapidly \n infer phylogenies for big sets of genomes. Because andi does not compute \n full alignments, it is so efficient that it scales even up to thousands \n of bacterial genomes."
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}

‎records/aragorn.json

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{
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"function": [
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{
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"input": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2044"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1929"
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}
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]
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}
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],
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"functionHandle": "summary",
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"functionName": [
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{
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"uri": "http://edamontology.org/operation_0464"
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}
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],
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"output": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2044"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1929"
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}
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]
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},
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{
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"dataType": {
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"uri": "http://edamontology.org/data_0880"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_2076"
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}
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]
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}
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]
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}
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],
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"sourceRegistry": "",
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"name": "aragorn",
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"collection": "DebianMed",
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"topic": [
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{
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"uri": "http://edamontology.org/topic_0659"
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}
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],
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"version": "1.2.38-1",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/nar/gkh152"
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]
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},
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"homepage": "http://mbio-serv2.mbioekol.lu.se/ARAGORN/",
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"description": "tRNA and tmRNA detection in nucleotide sequences\n The program employs heuristic algorithms to predict tRNA secondary structure,\n based on homology with recognized tRNA consensus sequences and ability to form\n a base-paired cloverleaf. tmRNA genes are identified using a modified version\n of the BRUCE program."
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}

‎records/arden.json

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{
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"function": [
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{
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"input": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2044"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_1929"
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}
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]
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}
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],
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"functionHandle": "summary",
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"functionName": [
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{
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"uri": null
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}
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],
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"output": [
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{
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"dataType": {
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"uri": "http://edamontology.org/data_2048"
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},
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"dataFormat": [
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{
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"uri": "http://edamontology.org/format_2330"
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}
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]
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}
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]
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}
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],
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"sourceRegistry": "",
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"name": "ARDEN",
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"collection": "DebianMed",
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"topic": [
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{
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"uri": "http://edamontology.org/topic_3168"
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}
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],
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"version": "1.0-2",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/bioinformatics/btt255"
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]
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},
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"homepage": "http://sourceforge.net/projects/arden/",
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"description": "specificity control for read alignments using an artificial reference\n ARDEN (Artificial Reference Driven Estimation of false positives in NGS\n data) is a novel benchmark that estimates error rates based on real\n experimental reads and an additionally generated artificial reference\n genome. It allows the computation of error rates specifically for a\n dataset and the construction of a ROC-curve. Thereby, it can be used to\n optimize parameters for read mappers, to select read mappers for a\n specific problem or also to filter alignments based on quality\n estimation."
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}

‎records/ariba.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "ariba",
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"collection": "DebianMed",
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"version": "2.6.1+ds-1",
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"publications": {
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"publicationsPrimaryID": "None"
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},
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"homepage": "https://github.com/sanger-pathogens/ariba",
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"description": "Antibiotic Resistance Identification By Assembly\n ARIBA is a tool that identifies antibiotic resistance genes by running local\n assemblies.\n The input is a FASTA file of reference genes and paired sequencing reads. ARIBA\n reports which of the reference genes were found, plus detailed information on\n the quality of the assemblies and any variants between the sequencing reads\n and the reference genes."
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}

‎records/art-nextgen-simulation-tools.json

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{
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"function": [],
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"sourceRegistry": "",
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"name": "ART",
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"collection": "DebianMed",
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"version": "20160605+dfsg-2",
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"publications": {
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"publicationsPrimaryID": [
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"10.1093/bioinformatics/btr708"
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]
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},
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"homepage": "http://www.niehs.nih.gov/research/resources/software/biostatistics/art/",
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"description": "simulation tools to generate synthetic next-generation sequencing reads\n ART is a set of simulation tools to generate synthetic next-generation\n sequencing reads. ART simulates sequencing reads by mimicking real\n sequencing process with empirical error models or quality profiles\n summarized from large recalibrated sequencing data. ART can also\n simulate reads using user own read error model or quality profiles. ART\n supports simulation of single-end, paired-end/mate-pair reads of three\n major commercial next-generation sequencing platforms: Illumina's\n Solexa, Roche's 454 and Applied Biosystems' SOLiD. ART can be used to\n test or benchmark a variety of method or tools for next-generation\n sequencing data analysis, including read alignment, de novo assembly,\n SNP and structure variation discovery. ART was used as a primary tool\n for the simulation study of the 1000 Genomes Project . ART is\n implemented in C++ with optimized algorithms and is highly efficient in\n read simulation. ART outputs reads in the FASTQ format, and alignments\n in the ALN format. ART can also generate alignments in the SAM\n alignment or UCSC BED file format. ART can be used together with genome\n variants simulators (e.g. VarSim) for evaluating variant calling tools\n or methods."
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}

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