MuG - FASTQ Pipelines
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Contents:
Requirements and Installation
Full Installation
Pipelines
Tools for processing FastQ files
Utility Functions
Continuous Integration with Travis
Setting up and using a Docker Container
Architectural Design Record
License
Test Datasets:
Testing
Test Data for ChIP-seq pipeline
iDamID-Seq Test Data
Test Data for MNase-seq pipeline
Test Data for RNA-seq pipeline
WGBS Test Data
Hi-C Test Data
MuG - FASTQ Pipelines
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A
alignerUtils (class in tool.aligner_utils)
all_toolchain() (in module tests.test_toolchains)
B
bam_copy() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_count_reads() (tool.bam_utils.bamUtils static method)
bam_filter() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_index() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_list_chromosomes() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_merge() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_merge_10() (tool.bam_utils.bamUtilsTask method)
bam_merge_2() (tool.bam_utils.bamUtilsTask method)
bam_merge_3() (tool.bam_utils.bamUtilsTask method)
bam_merge_4() (tool.bam_utils.bamUtilsTask method)
bam_merge_5() (tool.bam_utils.bamUtilsTask method)
bam_paired_reads() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_sort() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_split() (tool.bam_utils.bamUtils static method)
bam_stats() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
bam_to_bed() (tool.bam_utils.bamUtils static method)
bamUtils (class in tool.bam_utils)
bamUtilsTask (class in tool.bam_utils)
biobambam (class in tool.biobambam_filter)
biobambam_filter_alignments() (tool.biobambam_filter.biobambam method)
biobambam_toolchain() (in module tests.test_toolchains)
bowtie2_align_reads() (tool.aligner_utils.alignerUtils static method)
bowtie2_aligner_paired() (tool.bowtie_aligner.bowtie2AlignerTool method)
bowtie2_aligner_single() (tool.bowtie_aligner.bowtie2AlignerTool method)
bowtie2_indexer() (tool.bowtie_indexer.bowtieIndexerTool method)
bowtie2_toolchain() (in module tests.test_toolchains)
bowtie2_untar_index() (tool.aligner_utils.alignerUtils method)
bowtie2AlignerTool (class in tool.bowtie_aligner)
bowtie_index_genome() (tool.aligner_utils.alignerUtils static method)
bowtieIndexerTool (class in tool.bowtie_indexer)
bs_seeker_aligner() (tool.bs_seeker_aligner.bssAlignerTool method)
bs_seeker_aligner_single() (tool.bs_seeker_aligner.bssAlignerTool method)
bsgenome_creater() (tool.forge_bsgenome.bsgenomeTool method)
bsgenomeTool (class in tool.forge_bsgenome)
bss_build_index() (tool.bs_seeker_indexer.bssIndexerTool method)
bss_seeker_filter() (tool.bs_seeker_filter.filterReadsTool method)
bssAlignerTool (class in tool.bs_seeker_aligner)
bssIndexerTool (class in tool.bs_seeker_indexer)
bwa_aligner_paired() (tool.bwa_aligner.bwaAlignerTool method)
(tool.bwa_mem_aligner.bwaAlignerMEMTool method)
bwa_aligner_single() (tool.bwa_aligner.bwaAlignerTool method)
(tool.bwa_mem_aligner.bwaAlignerMEMTool method)
bwa_aln_align_reads_paired() (tool.aligner_utils.alignerUtils method)
bwa_aln_align_reads_single() (tool.aligner_utils.alignerUtils method)
bwa_index_genome() (tool.aligner_utils.alignerUtils static method)
bwa_indexer() (tool.bwa_indexer.bwaIndexerTool method)
bwa_mem_align_reads() (tool.aligner_utils.alignerUtils static method)
bwa_toolchain() (in module tests.test_toolchains)
bwa_untar_index() (tool.aligner_utils.alignerUtils method)
bwaAlignerMEMTool (class in tool.bwa_mem_aligner)
bwaAlignerTool (class in tool.bwa_aligner)
bwaIndexerTool (class in tool.bwa_indexer)
C
cd (class in tool.common)
check_header() (tool.bam_utils.bamUtils static method)
(tool.bam_utils.bamUtilsTask method)
chipseq_toolchain() (in module tests.test_toolchains)
closeFastQ() (tool.fastqreader.fastqreader method)
closeOutputFiles() (tool.fastqreader.fastqreader method)
createOutputFiles() (tool.fastqreader.fastqreader method)
E
eof() (tool.fastqreader.fastqreader method)
F
fastq_match_paired_ends() (tool.fastq_utils.fastqUtils static method)
fastq_randomise() (tool.fastq_utils.fastqUtils static method)
fastq_sort_file() (tool.fastq_utils.fastqUtils static method)
fastq_splitter (class in tool.fastq_splitter)
fastqcTool (class in tool.validate_fastqc)
fastqreader (class in tool.fastqreader)
fastqUtils (class in tool.fastq_utils)
filterReadsTool (class in tool.bs_seeker_filter)
G
gem_index_genome() (tool.aligner_utils.alignerUtils static method)
gem_indexer() (tool.gem_indexer.gemIndexerTool method)
gemIndexerTool (class in tool.gem_indexer)
genome_to_2bit() (tool.forge_bsgenome.bsgenomeTool static method)
genome_toolchain() (in module tests.test_toolchains)
get_aln_params() (tool.bowtie_aligner.bowtie2AlignerTool static method)
(tool.bs_seeker_aligner.bssAlignerTool static method)
(tool.bwa_aligner.bwaAlignerTool static method)
get_bss_index_params() (tool.bs_seeker_indexer.bssIndexerTool static method)
get_chrom_size() (tool.forge_bsgenome.bsgenomeTool static method)
get_macs2_params() (tool.macs2.macs2 static method)
get_mem_params() (tool.bwa_mem_aligner.bwaAlignerMEMTool static method)
get_trimgalore_params() (tool.trimgalore.trimgalore static method)
,
[1]
H
hic_toolchain() (in module tests.test_toolchains)
I
idamidseq_toolchain() (in module tests.test_toolchains)
idear_peak_calling() (tool.idear.idearTool method)
idearTool (class in tool.idear)
incrementOutputFiles() (tool.fastqreader.fastqreader method)
inps (class in tool.inps)
inps_peak_calling() (tool.inps.inps method)
K
kallisto_indexer() (tool.kallisto_indexer.kallistoIndexerTool method)
kallisto_quant_paired() (tool.kallisto_quant.kallistoQuantificationTool method)
kallisto_quant_single() (tool.kallisto_quant.kallistoQuantificationTool method)
kallisto_tsv2bed() (tool.kallisto_quant.kallistoQuantificationTool method)
kallisto_tsv2gff() (tool.kallisto_quant.kallistoQuantificationTool method)
kallistoIndexerTool (class in tool.kallisto_indexer)
kallistoQuantificationTool (class in tool.kallisto_quant)
L
load_gff_ensembl() (tool.kallisto_quant.kallistoQuantificationTool static method)
load_gff_ucsc() (tool.kallisto_quant.kallistoQuantificationTool static method)
M
macs2 (class in tool.macs2)
macs2_peak_calling() (tool.macs2.macs2 method)
macs2_peak_calling_nobgd() (tool.macs2.macs2 method)
mnaseseq_toolchain() (in module tests.test_toolchains)
N
next() (tool.fastqreader.fastqreader method)
O
openFastQ() (tool.fastqreader.fastqreader method)
P
paired_splitter() (tool.fastq_splitter.fastq_splitter method)
process_align_bowtie (module)
process_align_bwa (module)
process_align_bwa_mem (module)
process_biobambam (class in process_biobambam)
(module)
process_bowtie (class in process_align_bowtie)
process_bs_seeker_aligner (class in process_bs_seeker_aligner)
(module)
process_bs_seeker_filter (module)
process_bs_seeker_index (class in process_bs_seeker_index)
(module)
process_bsFilter (class in process_bs_seeker_filter)
process_bsgenome (class in process_bsgenome)
(module)
process_bwa (class in process_align_bwa)
process_bwa_mem (class in process_align_bwa_mem)
process_chipseq (class in process_chipseq)
(module)
process_damidseq (class in process_damidseq)
(module)
process_genome (class in process_genome)
(module)
process_hic (class in process_hic)
(module)
process_iNPS (class in process_iNPS)
(module)
process_macs2 (class in process_macs2)
(module)
process_mnaseseq (class in process_mnaseseq)
(module)
process_rnaseq (class in process_rnaseq)
(module)
process_trim_galore (class in process_trim_galore)
(module)
R
replaceENAHeader() (tool.aligner_utils.alignerUtils static method)
rnaseq_toolchain() (in module tests.test_toolchains)
run() (process_align_bowtie.process_bowtie method)
(process_align_bwa.process_bwa method)
(process_align_bwa_mem.process_bwa_mem method)
(process_biobambam.process_biobambam method)
(process_bs_seeker_aligner.process_bs_seeker_aligner method)
(process_bs_seeker_filter.process_bsFilter method)
(process_bs_seeker_index.process_bs_seeker_index method)
(process_bsgenome.process_bsgenome method)
(process_chipseq.process_chipseq method)
(process_damidseq.process_damidseq method)
(process_genome.process_genome method)
(process_hic.process_hic method)
(process_iNPS.process_iNPS method)
(process_macs2.process_macs2 method)
(process_mnaseseq.process_mnaseseq method)
(process_rnaseq.process_rnaseq method)
(process_trim_galore.process_trim_galore method)
(tool.biobambam_filter.biobambam method)
(tool.bowtie_aligner.bowtie2AlignerTool method)
(tool.bowtie_indexer.bowtieIndexerTool method)
(tool.bs_seeker_aligner.bssAlignerTool method)
(tool.bs_seeker_filter.filterReadsTool method)
(tool.bs_seeker_indexer.bssIndexerTool method)
(tool.bwa_aligner.bwaAlignerTool method)
(tool.bwa_indexer.bwaIndexerTool method)
(tool.bwa_mem_aligner.bwaAlignerMEMTool method)
(tool.fastq_splitter.fastq_splitter method)
(tool.forge_bsgenome.bsgenomeTool method)
(tool.gem_indexer.gemIndexerTool method)
(tool.idear.idearTool method)
(tool.inps.inps method)
(tool.kallisto_indexer.kallistoIndexerTool method)
(tool.kallisto_quant.kallistoQuantificationTool method)
(tool.macs2.macs2 method)
(tool.tb_bin.tbBinTool method)
(tool.tb_filter.tbFilterTool method)
(tool.tb_full_mapping.tbFullMappingTool method)
(tool.tb_generate_tads.tbGenerateTADsTool method)
(tool.tb_model.tbModelTool method)
(tool.tb_normalize.tbNormalizeTool method)
(tool.tb_parse_mapping.tbParseMappingTool method)
(tool.tb_save_hdf5_matrix.tbSaveAdjacencyHDF5Tool method)
(tool.tb_segment.tbSegmentTool method)
(tool.trimgalore.trimgalore method)
,
[1]
(tool.validate_fastqc.fastqcTool method)
run_aligner() (tool.bs_seeker_aligner.bssAlignerTool method)
S
sam_to_bam() (tool.bam_utils.bamUtils static method)
seq_read_stats() (tool.kallisto_quant.kallistoQuantificationTool static method)
single_splitter() (tool.fastq_splitter.fastq_splitter method)
T
tb_bin() (tool.tb_bin.tbBinTool method)
tb_filter() (tool.tb_filter.tbFilterTool method)
tb_full_mapping_frag() (tool.tb_full_mapping.tbFullMappingTool method)
tb_full_mapping_iter() (tool.tb_full_mapping.tbFullMappingTool method)
tb_generate_tads() (tool.tb_generate_tads.tbGenerateTADsTool method)
tb_hic_chr() (tool.tb_generate_tads.tbGenerateTADsTool method)
tb_matrix_hdf5() (tool.tb_save_hdf5_matrix.tbSaveAdjacencyHDF5Tool method)
tb_merge_tad_files() (tool.tb_generate_tads.tbGenerateTADsTool method)
tb_model() (tool.tb_model.tbModelTool method)
tb_normalize() (tool.tb_normalize.tbNormalizeTool method)
tb_parse_mapping_frag() (tool.tb_parse_mapping.tbParseMappingTool method)
tb_parse_mapping_iter() (tool.tb_parse_mapping.tbParseMappingTool method)
tb_segment() (tool.tb_segment.tbSegmentTool method)
tbBinTool (class in tool.tb_bin)
tbFilterTool (class in tool.tb_filter)
tbFullMappingTool (class in tool.tb_full_mapping)
tbGenerateTADsTool (class in tool.tb_generate_tads)
tbModelTool (class in tool.tb_model)
tbNormalizeTool (class in tool.tb_normalize)
tbParseMappingTool (class in tool.tb_parse_mapping)
tbSaveAdjacencyHDF5Tool (class in tool.tb_save_hdf5_matrix)
tbSegmentTool (class in tool.tb_segment)
test_chipseq_pipeline_00() (in module tests.test_pipeline_chipseq)
test_chipseq_pipeline_01() (in module tests.test_pipeline_chipseq)
test_genome_pipeline_00() (in module tests.test_pipeline_genome)
test_genome_pipeline_01() (in module tests.test_pipeline_genome)
test_idamidseq_pipeline_00() (in module tests.test_pipeline_idamidseq)
test_idamidseq_pipeline_01() (in module tests.test_pipeline_idamidseq)
test_mnaseseq_pipeline() (in module tests.test_pipeline_mnaseseq)
test_rnaseq_pipeline() (in module tests.test_pipeline_rnaseq)
test_tb_pipeline() (in module tests.test_pipeline_tb)
tests (module)
tests.test_pipeline_chipseq (module)
tests.test_pipeline_genome (module)
tests.test_pipeline_idamidseq (module)
tests.test_pipeline_mnaseseq (module)
tests.test_pipeline_rnaseq (module)
tests.test_pipeline_tb (module)
tests.test_toolchains (module)
tidy_data() (in module tests.test_toolchains)
tool (module)
,
[1]
trimgalore (class in tool.trimgalore)
,
[1]
trimgalore_paired() (tool.trimgalore.trimgalore method)
,
[1]
trimgalore_single() (tool.trimgalore.trimgalore method)
,
[1]
trimgalore_version() (tool.trimgalore.trimgalore method)
,
[1]
U
untar_index() (tool.bowtie_aligner.bowtie2AlignerTool method)
(tool.bwa_aligner.bwaAlignerTool method)
(tool.bwa_mem_aligner.bwaAlignerMEMTool method)
V
validate() (tool.validate_fastqc.fastqcTool method)
W
wgbs_toolchain() (in module tests.test_toolchains)
writeOutput() (tool.fastqreader.fastqreader method)
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