seq_crumbs protocols

View seq_crumbs computational protocol

seq_crumbs statistics

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seq_crumbs specifications

Information


Unique identifier OMICS_01075
Name seq_crumbs
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • sff_extract

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seq_crumbs in pipelines

 (4)
2017
PMCID: 5522415
PMID: 28733645
DOI: 10.1038/s41467-017-00182-7

[…] reagents. sequencing data were processed using the illumina pipeline casava 1.82. purity-filtered reads were adapter and quality trimmed with cutadapt (v. 1.3, and filtered for low complexity with seq_crumbs (v. 0.1.8). reads were aligned against mus musculus (version grcm38) genome using star (v. 2.4.2a,. the number of read counts per gene locus was summarized with htseq-count (v. 0.6.1,) […]

2015
PMCID: 4395073
PMID: 25792047
DOI: 10.1128/genomeA.00109-15

[…] a 454 pyrosequencing method and pacbio smrt technology to provide both high coverage and high-quality contigs (). the 454 reads (191,539 reads) have been converted to the fastq format using the seq_crumbs package (version 0.1.8; http://bioinf.comav.upv.es/seq_crumbs/) and trimmed using streamingtrim (version 1.0) (). both 454 and pacbio reads quality has been checked using fastqc (version […]

2015
PMCID: 4552406
PMID: 26315384
DOI: 10.1186/s12864-015-1859-8

[…] were sequenced by an illumina miseq sequencer. a total of eight different datasets of paired-end 2 x 250 bp reads were generated (srp060735). for sequence quality estimation, calculate_stats from seq_crumbs was used to estimate the read qualities for each dataset []. for further de novo assembly analysis, reads were trimmed to fit the quality threshold of phred quality scores larger than q20 […]

2014
PMCID: 3997825
PMID: 24690220
DOI: 10.1186/1756-3305-7-151

[…] prior to assembly. relevant adapter sequences were removed with cutadapt [], and reads with an overall quality score less than 20 and an overall dust score less than seven were removed using seq_crumbs software (http://bioinf.comav.upv.es/seq_crumbs/). the remaining reads were aligned to rrna [,] and bacterial [] sequence databases with bowtie2 (version 2.1.0, default parameters []) […]


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seq_crumbs in publications

 (12)
PMCID: 5787289
PMID: 29374454
DOI: 10.1186/s12870-018-1237-1

[…] (http://hannonlab.cshl.edu/fastx_toolkit) with a minimum quality score of 25 and a minimum length of 40. adaptor sequences were trimmed using the ‘trim_blast_short’ script available as part of seq_crumbs (http://bioinf.comav.upv.es/seq_crumbs/). high quality reads of all samples were combined in order to perform the de novo assembly using the trinity v.20140413p1 software [] (see […]

PMCID: 5703900
PMID: 29180618
DOI: 10.1038/s41467-017-01804-w

[…] selection. libraries were sequenced with the illumina hiseq2000 (1 × 100 bp). purity-filtered reads were adapter and quality trimmed with cutadapt (v. 1.3), and filtered for low complexity with seq_crumbs (v. 0.1.8). reads were aligned against the mus musculus.grcm38.82 genome using star (v. 2.4.2a). the number of read counts per gene locus was summarized with htseq-count (v. 0.6.1) using […]

PMCID: 5582342
PMID: 28912788
DOI: 10.3389/fpls.2017.01477

[…] that presented less coverage than 15, a mapping quality of 20 or a base quality of 20. in order to select the most reliable snps for genotyping the plants with hrm, different filters from the seq crumbs tools (https://bioinf.comav.upv.es/seq_crumbs/) were applied to the vcf file for maximizing the polymorphism validation. the filters cs60 and cl60 identified polymorphisms […]

PMCID: 5536302
PMID: 28759564
DOI: 10.1371/journal.pone.0179061

[…] leading:30 trailing:30 minlen:25. cleaned paired reads were concatenated across both samples to form combined left.fastq and right.fastq files. the calculate_stats utility from seq_crumbs was used to calculate q20 and q30 using the command calculate_stats–c [left.fastq,right.fastq] > out.txt []. cleaned paired reads were combined across both samples and passed to trinity […]

PMCID: 5522415
PMID: 28733645
DOI: 10.1038/s41467-017-00182-7

[…] reagents. sequencing data were processed using the illumina pipeline casava 1.82. purity-filtered reads were adapter and quality trimmed with cutadapt (v. 1.3, and filtered for low complexity with seq_crumbs (v. 0.1.8). reads were aligned against mus musculus (version grcm38) genome using star (v. 2.4.2a,. the number of read counts per gene locus was summarized with htseq-count (v. 0.6.1,) […]


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