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  jeremiahsavage

  Joined on Dec 14, 2015

42 projects

picard_metrics_sqlite

Last released on Apr 19, 2018

store picard metrics in sqlite

fastq_to_SAM_PU

Last released on Feb 2, 2018

extract a PU value from a fastq record

json-to-sqlite

Last released on Jan 18, 2018

convert to json to column based sqlite

integrity_to_sqlite

Last released on Jan 17, 2018

store `ls -l`, `md5sum` and `sha256sum` to sqlite

readgroup_json_db

Last released on Jan 17, 2018

read readgroup data as json and store in sqlitedb

merge_sqlite

Last released on Jan 17, 2018

merge arbitrary number of sqlite files

fastqc_db

Last released on Jan 17, 2018

store FastQC data/summary in sqlitedb

samtools_metrics_sqlite

Last released on Jan 17, 2018

store samtools metrics in sqlite

sqlite_to_postgres

Last released on Jan 11, 2018

write sqlite file to postgres

bunny_runtime_metrics_sqlite

Last released on Sep 21, 2017

store bunny runtime metrics in sqlite

star_metrics_sqlite

Last released on Jul 20, 2017

store star metrics in sqlite

fastqvalidator_sqlite

Last released on Jul 19, 2017

store fastqvalidator metrics in sqlite

bam_readgroup_to_json

Last released on Jul 3, 2017

convert each readgroup id to a json file from a BAM

dnaseq_queue_status

Last released on May 31, 2017

write db status

dnaseq_validation

Last released on May 9, 2017

validate dnaseq workflow based on fastqc, picard and samtools metrics

queue_bqsr_status

Last released on Mar 29, 2017

write bqsr db status

table_string_sqlite_cell

Last released on Mar 27, 2017

create a single cell table with a value

optityper_to_sqlite

Last released on Feb 4, 2017

store optityper metrics in sqlite

queue_hlatype_status

Last released on Feb 3, 2017

write hlatyping db status

queue_coclean_status

Last released on Jan 30, 2017

write coclean db status

fastqc_to_json

Last released on Nov 15, 2016

fastqc to json for bwa cwl

queue_status

Last released on Sep 29, 2016

write db status

cgquery_xml_to_bamlibrary_capture_json

Last released on Sep 21, 2016

convert cgquery sra xml to capture_kits/target_set json

fastq_remove_duplicate_qname

Last released on Aug 31, 2016

remove duplicate QNAME from a fastq

bam_reheader

Last released on Aug 26, 2016

reheader a BAM to include GDC @SQ info

picard_tool

Last released on Jul 26, 2016

call picard tools and store time/mem metrics in sqlitedb

bwa_pe_tool

Last released on Jul 11, 2016

map PE fastq reads to a reference genome with bwa

decider_bwa_pe

Last released on Jul 11, 2016

match readgroup and fastq outputs

decider_bwa_se

Last released on Jul 11, 2016

match readgroup and fastq outputs

bwa_tool

Last released on Jun 30, 2016

map PE fastq reads to a reference genome with bwa

bwa_se_tool

Last released on Jun 29, 2016

map SE fastq reads to a reference genome with bwa

bam_add_eof

Last released on Jun 24, 2016

if a BAM is missing EOF, add it, else output original BAM

remove_duplicate_fastq_matepair

Last released on Jun 24, 2016

Remove duplicate mate pairs from a FASTQ

fastqc_tool

Last released on Jun 15, 2016

call fastqc tools and store time/mem metrics in sqlitedb

biobambam_tool

Last released on Jun 15, 2016

call biobambam tools and store time/mem metrics in sqlitedb

samtools_tool

Last released on Jun 15, 2016

call samtools tools and store time/mem metrics in sqlitedb

cdis_pipe_utils

Last released on Jun 13, 2016

Reusable code to call pipeline tools and get time/mem metrics

fastqc_sqlite

Last released on Apr 19, 2016

store FastQC data/summary in sqlitedb

readgroup_platform_insertion

Last released on Mar 23, 2016

Insert a PL:<value> in @RGs in a BAM header

sra_hs_lookup

Last released on Jan 4, 2016

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

remove_qcfailed_mapped

Last released on Jan 4, 2016

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

bamutil_tool

Last released on Dec 17, 2015

call bamutil tools and store time/mem metrics in sqlitedb

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