/
container.yaml
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/
container.yaml
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url: https://biocontainers.pro/tools/masurca
maintainer: '@vsoch'
description: shpc-registry automated BioContainers addition for masurca
latest:
4.1.0--pl5321hb5bd705_1: sha256:8f2a650c98c2f84c2be6a8ad2f47855d2d639c52b6717752277a0e2a4dd7a6e4
tags:
4.0.9--pl5321h6e1a2d6_1: sha256:51e3f4c3b5bfa20f6ec2059f5ce04ac25c1a3a9dc599085a7e3054cb0952f7c2
4.1.0--pl5321h6e1a2d6_0: sha256:472dc29e5b23be97f13559a5fbaa6a9e3558d865783a846fe354d9c84d1cb1fc
4.1.0--pl5321hb5bd705_1: sha256:8f2a650c98c2f84c2be6a8ad2f47855d2d639c52b6717752277a0e2a4dd7a6e4
docker: quay.io/biocontainers/masurca
aliases:
MasurcaCelera.pm: /usr/local/bin/MasurcaCelera.pm
MasurcaCommon.pm: /usr/local/bin/MasurcaCommon.pm
MasurcaConf.pm: /usr/local/bin/MasurcaConf.pm
MasurcaPaths.pm: /usr/local/bin/MasurcaPaths.pm
MasurcaSoap.pm: /usr/local/bin/MasurcaSoap.pm
MasurcaSuperReads.pm: /usr/local/bin/MasurcaSuperReads.pm
SOAPdenovo-127mer: /usr/local/bin/SOAPdenovo-127mer
SOAPdenovo-63mer: /usr/local/bin/SOAPdenovo-63mer
addSurrogatesToFrgCtgFile: /usr/local/bin/addSurrogatesToFrgCtgFile
addSurrogatesToFrgctg.perl: /usr/local/bin/addSurrogatesToFrgctg.perl
add_missing_mates.pl: /usr/local/bin/add_missing_mates.pl
add_pb_seq.pl: /usr/local/bin/add_pb_seq.pl
blast_self_alignment_filter.pl: /usr/local/bin/blast_self_alignment_filter.pl
bloom_query: /usr/local/bin/bloom_query
break_contigs.pl: /usr/local/bin/break_contigs.pl
build_human_reference.sh: /usr/local/bin/build_human_reference.sh
chromosome_scaffolder.sh: /usr/local/bin/chromosome_scaffolder.sh
classify_reads.pl: /usr/local/bin/classify_reads.pl
closeGaps.oneDirectory.fromMinKmerLen.perl: /usr/local/bin/closeGaps.oneDirectory.fromMinKmerLen.perl
closeGaps.oneDirectory.perl: /usr/local/bin/closeGaps.oneDirectory.perl
closeGaps.perl: /usr/local/bin/closeGaps.perl
closeGapsInScaffFastaFile.perl: /usr/local/bin/closeGapsInScaffFastaFile.perl
closeGapsLocally.perl: /usr/local/bin/closeGapsLocally.perl
close_gaps.sh: /usr/local/bin/close_gaps.sh
close_scaffold_gaps.sh: /usr/local/bin/close_scaffold_gaps.sh
collectReadSequencesForLocalGapClosing: /usr/local/bin/collectReadSequencesForLocalGapClosing
compute_coverage.pl: /usr/local/bin/compute_coverage.pl
compute_sr_cov.pl: /usr/local/bin/compute_sr_cov.pl
compute_sr_cov.revisedForGCContig.pl: /usr/local/bin/compute_sr_cov.revisedForGCContig.pl
correct_with_k_unitigs.sh: /usr/local/bin/correct_with_k_unitigs.sh
correct_with_k_unitigs_fast.pl: /usr/local/bin/correct_with_k_unitigs_fast.pl
createFastaSuperReadSequences: /usr/local/bin/createFastaSuperReadSequences
createKUnitigMaxOverlaps: /usr/local/bin/createKUnitigMaxOverlaps
createSuperReadSequenceAndPlacementFileFromCombined.perl: /usr/local/bin/createSuperReadSequenceAndPlacementFileFromCombined.perl
createSuperReadsForDirectory.perl: /usr/local/bin/createSuperReadsForDirectory.perl
create_end_pairs.perl: /usr/local/bin/create_end_pairs.perl
create_end_pairs.pl: /usr/local/bin/create_end_pairs.pl
create_k_unitigs_large_k: /usr/local/bin/create_k_unitigs_large_k
create_k_unitigs_large_k2: /usr/local/bin/create_k_unitigs_large_k2
create_mega_reads: /usr/local/bin/create_mega_reads
create_merged_mega-reads.pl: /usr/local/bin/create_merged_mega-reads.pl
create_merged_sequences.pl: /usr/local/bin/create_merged_sequences.pl
create_sr_frg: /usr/local/bin/create_sr_frg
create_sr_frg.pl: /usr/local/bin/create_sr_frg.pl
deduplicate_contigs.sh: /usr/local/bin/deduplicate_contigs.sh
deduplicate_unitigs.sh: /usr/local/bin/deduplicate_unitigs.sh
delta2vcf: /usr/local/bin/delta2vcf
determineUnjoinablePacbioSubmegas.perl: /usr/local/bin/determineUnjoinablePacbioSubmegas.perl
eliminateBadSuperReadsUsingList: /usr/local/bin/eliminateBadSuperReadsUsingList
error_corrected2frg: /usr/local/bin/error_corrected2frg
eugene.sh: /usr/local/bin/eugene.sh
evaluate_splits.pl: /usr/local/bin/evaluate_splits.pl
expand_fastq: /usr/local/bin/expand_fastq
extendSuperReadsBasedOnUniqueExtensions: /usr/local/bin/extendSuperReadsBasedOnUniqueExtensions
extendSuperReadsForUniqueKmerNeighbors: /usr/local/bin/extendSuperReadsForUniqueKmerNeighbors
extractJoinableAndNextPassReadsFromJoinKUnitigs.perl: /usr/local/bin/extractJoinableAndNextPassReadsFromJoinKUnitigs.perl
extract_chrM.sh: /usr/local/bin/extract_chrM.sh
extract_merges.pl: /usr/local/bin/extract_merges.pl
extract_merges_mega-reads.pl: /usr/local/bin/extract_merges_mega-reads.pl
extract_single_best_match_coords_file.pl: /usr/local/bin/extract_single_best_match_coords_file.pl
extract_unique_mega-reads.pl: /usr/local/bin/extract_unique_mega-reads.pl
extract_unjoined_pairs.pl: /usr/local/bin/extract_unjoined_pairs.pl
extractreads.pl: /usr/local/bin/extractreads.pl
extractreads_not.pl: /usr/local/bin/extractreads_not.pl
fasta2frg.pl: /usr/local/bin/fasta2frg.pl
fasta2frg_m.pl: /usr/local/bin/fasta2frg_m.pl
fasta_make_Nbase_bed.pl: /usr/local/bin/fasta_make_Nbase_bed.pl
fastqToFasta.pl: /usr/local/bin/fastqToFasta.pl
fill_unaligned_gaps.pl: /usr/local/bin/fill_unaligned_gaps.pl
filter_alt.pl: /usr/local/bin/filter_alt.pl
filter_delta_file_for_qrys.pl: /usr/local/bin/filter_delta_file_for_qrys.pl
filter_library.sh: /usr/local/bin/filter_library.sh
filter_overlap_file: /usr/local/bin/filter_overlap_file
filter_redundancy.pl: /usr/local/bin/filter_redundancy.pl
final_polish.sh: /usr/local/bin/final_polish.sh
findGapsInCoverageOfPacbios: /usr/local/bin/findGapsInCoverageOfPacbios
findMatchesBetweenKUnitigsAndReads: /usr/local/bin/findMatchesBetweenKUnitigsAndReads
find_contained_reads.pl: /usr/local/bin/find_contained_reads.pl
find_repeats.pl: /usr/local/bin/find_repeats.pl
fix_consensus_from_vcf.pl: /usr/local/bin/fix_consensus_from_vcf.pl
fix_unitigs.sh: /usr/local/bin/fix_unitigs.sh
fragScaff.pl: /usr/local/bin/fragScaff.pl
fragScaff.sh: /usr/local/bin/fragScaff.sh
getATBiasInCoverageForIllumina_v2: /usr/local/bin/getATBiasInCoverageForIllumina_v2
getEndSequencesOfContigs.perl: /usr/local/bin/getEndSequencesOfContigs.perl
getGCBiasStatistics.perl: /usr/local/bin/getGCBiasStatistics.perl
getLengthStatisticsForKUnitigsFile.perl: /usr/local/bin/getLengthStatisticsForKUnitigsFile.perl
getMeanAndStdevByGCCount.perl: /usr/local/bin/getMeanAndStdevByGCCount.perl
getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl: /usr/local/bin/getMeanAndStdevForGapsByGapNumUsingCeleraAsmFile.perl
getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory.perl: /usr/local/bin/getMeanAndStdevForGapsByGapNumUsingCeleraTerminatorDirectory.perl
getNumBasesPerReadInFastaFile.perl: /usr/local/bin/getNumBasesPerReadInFastaFile.perl
getSequenceForClosedGaps.perl: /usr/local/bin/getSequenceForClosedGaps.perl
getSequenceForLocallyClosedGaps.perl: /usr/local/bin/getSequenceForLocallyClosedGaps.perl
getSuperReadInsertCountsFromReadPlacementFile: /usr/local/bin/getSuperReadInsertCountsFromReadPlacementFile
getSuperReadInsertCountsFromReadPlacementFileTwoPasses: /usr/local/bin/getSuperReadInsertCountsFromReadPlacementFileTwoPasses
getSuperReadPlacements.perl: /usr/local/bin/getSuperReadPlacements.perl
getUnitigTypeFromAsmFile.perl: /usr/local/bin/getUnitigTypeFromAsmFile.perl
get_super_read_sizes: /usr/local/bin/get_super_read_sizes
get_super_read_sizes.pl: /usr/local/bin/get_super_read_sizes.pl
homo_trim: /usr/local/bin/homo_trim
insert_repeats.pl: /usr/local/bin/insert_repeats.pl
introduce_errors_fasta_file.pl: /usr/local/bin/introduce_errors_fasta_file.pl
jf_aligner: /usr/local/bin/jf_aligner
joinKUnitigs_v3: /usr/local/bin/joinKUnitigs_v3
join_mega_reads_trim.onepass.nomatch.pl: /usr/local/bin/join_mega_reads_trim.onepass.nomatch.pl
join_mega_reads_trim.onepass.pl: /usr/local/bin/join_mega_reads_trim.onepass.pl
join_mega_reads_trim.onepass.ref.pl: /usr/local/bin/join_mega_reads_trim.onepass.ref.pl
join_mega_reads_trim.onepass.rna.pl: /usr/local/bin/join_mega_reads_trim.onepass.rna.pl
killBadKUnitigs: /usr/local/bin/killBadKUnitigs
longest_path: /usr/local/bin/longest_path
makeAdjustmentFactorsForNumReadsForAStatBasedOnGC: /usr/local/bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC
makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2: /usr/local/bin/makeAdjustmentFactorsForNumReadsForAStatBasedOnGC_v2
make_mate_frg.pl: /usr/local/bin/make_mate_frg.pl
make_mr_frg.pl: /usr/local/bin/make_mr_frg.pl
make_rejoin_links.pl: /usr/local/bin/make_rejoin_links.pl
masurca: /usr/local/bin/masurca
masurca-superreads: /usr/local/bin/masurca-superreads
mega_reads_assemble_cluster.sh: /usr/local/bin/mega_reads_assemble_cluster.sh
mega_reads_assemble_cluster2.sh: /usr/local/bin/mega_reads_assemble_cluster2.sh
mega_reads_assemble_polish.sh: /usr/local/bin/mega_reads_assemble_polish.sh
mega_reads_assemble_ref.sh: /usr/local/bin/mega_reads_assemble_ref.sh
mergeSuperReadsUniquely.pl: /usr/local/bin/mergeSuperReadsUniquely.pl
merge_contigs.pl: /usr/local/bin/merge_contigs.pl
merge_coords: /usr/local/bin/merge_coords
merge_matches_and_tile_coords_file.pl: /usr/local/bin/merge_matches_and_tile_coords_file.pl
merge_mate_pairs: /usr/local/bin/merge_mate_pairs
merge_mega-reads.pl: /usr/local/bin/merge_mega-reads.pl
merge_sequences_simple.pl: /usr/local/bin/merge_sequences_simple.pl
my_maker_functional_fasta: /usr/local/bin/my_maker_functional_fasta
my_maker_functional_gff: /usr/local/bin/my_maker_functional_gff
outputAlekseysJellyfishReductionFile.perl: /usr/local/bin/outputAlekseysJellyfishReductionFile.perl
outputJoinedPairs.perl: /usr/local/bin/outputJoinedPairs.perl
outputRecordsNotOnList: /usr/local/bin/outputRecordsNotOnList
output_reconciled_scaffolds.pl: /usr/local/bin/output_reconciled_scaffolds.pl
parallel_delta-filter.sh: /usr/local/bin/parallel_delta-filter.sh
polca.sh: /usr/local/bin/polca.sh
polish_with_illumina_assembly.sh: /usr/local/bin/polish_with_illumina_assembly.sh
process_scaffold_gaps.pl: /usr/local/bin/process_scaffold_gaps.pl
quorum: /usr/local/bin/quorum
quorum_create_database: /usr/local/bin/quorum_create_database
quorum_error_correct_reads: /usr/local/bin/quorum_error_correct_reads
recompute_astat_superreads.sh: /usr/local/bin/recompute_astat_superreads.sh
recompute_astat_superreads_CA8.sh: /usr/local/bin/recompute_astat_superreads_CA8.sh
reconcile_alignments.sh: /usr/local/bin/reconcile_alignments.sh
reconcile_consensus.pl: /usr/local/bin/reconcile_consensus.pl
reconcile_matches.pl: /usr/local/bin/reconcile_matches.pl
reconciliate_mega_reads.maximal.nucmer.pl: /usr/local/bin/reconciliate_mega_reads.maximal.nucmer.pl
recover_scaffolds.pl: /usr/local/bin/recover_scaffolds.pl
reduce_sr: /usr/local/bin/reduce_sr
refine.sh: /usr/local/bin/refine.sh
refine_alignments.pl: /usr/local/bin/refine_alignments.pl
rename_filter_fastq: /usr/local/bin/rename_filter_fastq
rename_filter_fastq.pl: /usr/local/bin/rename_filter_fastq.pl
resolve_trio.sh: /usr/local/bin/resolve_trio.sh
restore_ns.pl: /usr/local/bin/restore_ns.pl
reverse_complement: /usr/local/bin/reverse_complement
runByDirectory: /usr/local/bin/runByDirectory
runSRCA.pl: /usr/local/bin/runSRCA.pl
run_ECR.sh: /usr/local/bin/run_ECR.sh
samToDelta: /usr/local/bin/samToDelta
samba.sh: /usr/local/bin/samba.sh
sample_mate_pairs.pl: /usr/local/bin/sample_mate_pairs.pl
sizesToScaff.pl: /usr/local/bin/sizesToScaff.pl
sorted_merge: /usr/local/bin/sorted_merge
splitFileAtNs: /usr/local/bin/splitFileAtNs
splitFileByPrefix.pl: /usr/local/bin/splitFileByPrefix.pl
splitLongKUnitigs.pl: /usr/local/bin/splitLongKUnitigs.pl
splitScaffoldsAtNs.pl: /usr/local/bin/splitScaffoldsAtNs.pl
splitScaffoldsAtNs.sh: /usr/local/bin/splitScaffoldsAtNs.sh
split_long_unitigs.pl: /usr/local/bin/split_long_unitigs.pl
split_matches_file.pl: /usr/local/bin/split_matches_file.pl
split_mate_pairs: /usr/local/bin/split_mate_pairs
split_reads_to_join.pl: /usr/local/bin/split_reads_to_join.pl
translateReduceFile.perl: /usr/local/bin/translateReduceFile.perl
translate_reduced_reads.pl: /usr/local/bin/translate_reduced_reads.pl
trim_by_kunitigs.pl: /usr/local/bin/trim_by_kunitigs.pl
trim_mega_reads.pl: /usr/local/bin/trim_mega_reads.pl
ufasta: /usr/local/bin/ufasta
egrep: /usr/local/bin/egrep
fgrep: /usr/local/bin/fgrep
grep: /usr/local/bin/grep
freebayes: /usr/local/bin/freebayes
jellyfish: /usr/local/bin/jellyfish
combineMUMs: /usr/local/bin/combineMUMs
delta-filter: /usr/local/bin/delta-filter
dnadiff: /usr/local/bin/dnadiff
exact-tandems: /usr/local/bin/exact-tandems
mummer: /usr/local/bin/mummer