Commit ad8c3635 authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/release' into 'dev'

Algo 2021.02.2

See merge request !917
parents cea776f5 0ad00681
Pipeline #217433 failed with stages
in 8 minutes and 35 seconds
......@@ -1247,7 +1247,7 @@ int main (int argc, char **argv)
//////////////////////////////////
string f_all_windows = out_dir + f_basename + WINDOWS_FILENAME;
std::ostream *out_all_windows = new_ofgzstream(f_all_windows, out_gz);
std::ostream *out_all_windows = new_ofgzstream(f_all_windows, false);
windowsStorage->printSortedWindows(*out_all_windows);
delete out_all_windows;
cout << endl;
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2021-02-18 The Vidjil Team
* New preset --filter-reads to filter potentially huge datasets (vidjil.cpp) #4681
* Better --gz option, outputting also .fa.gz and .affects.gz files (vidjil.cpp) #4692
* New and updated documentation
2021-02-05 The Vidjil Team
* New report of unproductivity causes in 'seg.junction.unproductive' (core/segment.cpp) #4599
* New fields in AIRR .tsv output, 'vj_in_frame', 'stop_codon', '{v,j}_support', '{v,d,j,cdr3}_sequence_{start,end}' (core/output.cpp) #3569 #4643
......
......@@ -88,54 +88,59 @@ BMC Genomics 2014, 15:409
## Some publications using Vidjil
Chrystelle Abdo et al.,
*Caution encouraged in next-generation sequencing immunogenetic analyses in acute lymphoblastic leukemia*
Blood, 2020, 136(9):1105–1107
*Caution encouraged in next-generation sequencing immunogenetic analyses in acute lymphoblastic leukemia*,
Blood, 2020, 136(9):1105–1107,
<https://doi.org/10.1182/blood.2020005613>
Jean-Sebastien Allain et al.,
*IGHV segment utilization in immunoglobulin gene rearrangement differentiates patients with anti-myelin-associated glycoprotein neuropathy from others immunoglobulin M-gammopathies*,
Haematologica, 2018, 103:e207-e210
Haematologica, 2018, 103:e207-e210,
<http://dx.doi.org/10.3324/haematol.2017.177444>
Jack Bartram et al.,
*High throughput sequencing in acute lymphoblastic leukemia reveals clonal architecture of central nervous system and bone marrow compartments*
*High throughput sequencing in acute lymphoblastic leukemia reveals clonal architecture of central nervous system and bone marrow compartments*,
Haematologica, 2018,
<https://dx.doi.org/10.3324%2Fhaematol.2017.174987>
Sébastien Bender et al.,
*Immunoglobulin variable domain high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome*
*Immunoglobulin variable domain high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome*,
Blood, 2020,
<https://doi.org/10.1182/blood.2019004197>
Monika Brüggemann et al., on behalf of the EuroClonality-NGS working group,
*Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study*
*Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study*,
Leukemia, 2019, 33, 2241–2253,
<https://doi.org/10.1038/s41375-019-0496-7>
Roberta Cavagna et al.,
*Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes*
*Capture-based Next-Generation Sequencing Improves the Identification of Immunoglobulin/T-Cell Receptor Clonal Markers and Gene Mutations in Adult Acute Lymphoblastic Leukemia Patients Lacking Molecular Probes*,
Cancers, 2020, 12(6), 1505,
<https://doi.org/10.3390/cancers12061505>
Rodolfo P. Correia et al.,
*High‐throughput sequencing of immunoglobulin heavy chain for minimal residual disease detection in B‐lymphoblastic leukemia*,
Int. Journal of Laboratory Hematology, 2021,
<https://doi.org/10.1111/ijlh.13453>
Frédéric Davi et al., on behalf of ERIC, the European Research Initiative on CLL, and the EuroClonality-NGS Working Group,
*Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing*
*Immunoglobulin gene analysis in chronic lymphocytic leukemia in the era of next generation sequencing*,
2020
Leukemia, 2020,
<https://doi.org/10.1038/s41375-020-0923-9>
Yann Ferret et al.,
*Multi-loci diagnosis of acute lymphoblastic leukaemia with high-throughput sequencing and bioinformatics analysis*,
British Journal of Haematology, 2016, 173, 413–420
British Journal of Haematology, 2016, 173, 413–420,
<https://hal.archives-ouvertes.fr/hal-01279160>
Henrike J. Fischer et al.,
*Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion*
Journal of Neuroimmunology, 2015, S0165-5728(15)30065-5
*Modulation of CNS autoimmune responses by CD8+ T cells coincides with their oligoclonal expansion*,
Journal of Neuroimmunology, 2015, S0165-5728(15)30065-5,
<http://dx.doi.org/10.1016/j.jneuroim.2015.10.020>
Navarro Nilo Giusti et al., 2020
*Test trial of spike-in immunoglobulin heavy-chain (IGH) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia*
British Journal of Haematology, 2020, 189: e150-e154
*Test trial of spike-in immunoglobulin heavy-chain (IGH) controls for next generation sequencing quantification of minimal residual disease in acute lymphoblastic leukaemia*,
British Journal of Haematology, 2020, 189: e150-e154,
<https://doi.org/10.1111/bjh.16571>
Irene Jo et al.,
......@@ -144,40 +149,50 @@ Clinica Chimica Acta, 2019,
<https://doi.org/10.1016/j.cca.2018.10.037>
Takashi Kanamori et al.,
*Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort*
*Genomic analysis of multiple myeloma using targeted capture sequencing in the Japanese cohort*,
British Journal of Haematology, 2020,
<https://doi.org/10.1111/bjh.16720>
Kenji Kimura et al.,
*Identification of Clonal Immunoglobulin λ Light-Chain Gene Rearrangements in AL Amyloidosis Using Next Generation Sequencing*,
ASH 2019, Blood,
ASH 2019, Blood, 134(S1):1748,
<https://doi.org/10.1182/blood-2019-125028>
Michaela Kotrova et al.,
*The predictive strength of next-generation sequencing MRD detection for relapse compared with current methods in childhood ALL*,
Blood, 2015, 126:1045-1047
Blood, 2015, 126:1045-1047,
<http://dx.doi.org/10.1182/blood-2015-07-655159>
Michaela Kotrova et al.,
*Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell prolymphocytic leukemia cases*,
*Next‐generation amplicon TRB locus sequencing can overcome limitations of flow‐cytometric Vβ expression analysis and confirms clonality in all T‐cell ,prolymphocytic leukemia cases*,
Cytometry Part A, 93(11):1118-1124, 2018
<http://dx.doi.org/10.1002/cyto.a.23604>
Zhenhua Li et al.,
*Identifying IGH disease clones for MRD monitoring in childhood B-cell acute lymphoblastic leukemia using RNA-Seq*n
Leukemia, 2020, 34:2418-2429
*Identifying IGH disease clones for MRD monitoring in childhood B-cell acute lymphoblastic leukemia using RNA-Seq*,
Leukemia, 2020, 34:2418-2429,
<http://dx.doi.org/10.1038/s41375-020-0774-4>
Ralf A. Linker et al.,
*Thymocyte-derived BDNF influences T-cell maturation at the DN3/DN4 transition stage*,
European Journal of Immunology, 2015, 45, 1326-1338
European Journal of Immunology, 2015, 45, 1326-1338,
<http://dx.doi.org/10.1002/eji.201444985>
Ming Liang Oon et al.,
*T-Cell Lymphoma Clonality by Copy Number Variation Analysis of T-Cell Receptor Genes*,
Cancers, 2021, 13(2), 340
Cancers, 2021, 13(2), 340,
<https://dx.doi.org/10.3390/cancers13020340>
Alejandro Medina et al.,
*Comparison of next-generation sequencing (NGS) and next-generation flow (NGF) for minimal residual disease (MRD) assessment in multiple myeloma*,
Blood Cancer Journal, 10, 108,
<https://doi.org/10.1038/s41408-020-00377-0>
Dai Nishijima et al.,
*Capture Sequencing Is a Useful Method for Comprehensive Clonality Analysis Based on Ig/TCR Gene Rearrangements in Acute Lymphoblastic Leukemia*,
ASH 2018, Blood, 132(S1):1543,
<https://doi.org/10.1182/blood-2018-99-115624>
Edit Porpaczy et al.,
*Aggressive B-cell lymphomas in patients with myelofibrosis receiving JAK1/2 inhibitor therapy*,
Blood, 2018,
......@@ -185,36 +200,36 @@ Blood, 2018,
Mikaël Salson et al.,
*High-throughput sequencing in acute lymphoblastic leukemia: Follow-up of minimal residual disease and emergence of new clones*,
Leukemia Research, 2017, 53, 1–7
Leukemia Research, 2017, 53, 1–7,
<http://dx.doi.org/10.1016/j.leukres.2016.11.009>
Masashi Sanada et al.,
*Targeted-Capture Sequencing Is a Useful Method for MRD Markers Screening in KMT2A (MLL) Rearranged Leukemia*,
ASH 2019, Blood, 134(S1):2759
ASH 2019, Blood, 134(S1):2759,
<https://doi.org/10.1182/blood-2019-125421>
Florian Scherer et al.,
*Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA*,
Science Translational Medicine, 2016, 8, 364ra155
Science Translational Medicine, 2016, 8, 364ra155,
<http://dx.doi.org/10.1126/scitranslmed.aai8545>
V. Seitz et al.,
*Evidence for a role of RUNX1 as recombinase cofactor for TCRβ rearrangements and pathological deletions in ETV6-RUNX1 ALL*
Scientific Reports, 2020, 10: 10024
Scientific Reports, 2020, 10:10024,
<https://doi.org/10.1038/s41598-020-65744-0>
Udo zur Stadt et al.,
*Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL*
*Characterization of novel, recurrent genomic rearrangements as sensitive MRD targets in childhood B-cell precursor ALL*,
Blood Cancer Journal, 2019,
<https://doi.org/10.1038/s41408-019-0257-x>
Lucia Stranavova et al.,
*Heterologous Cytomegalovirus and Allo-Reactivity by Shared T Cell Receptor Repertoire in Kidney Transplantation*
*Heterologous Cytomegalovirus and Allo-Reactivity by Shared T Cell Receptor Repertoire in Kidney Transplantation*,
Frontiers in Immunology, 2019,
<https://doi.org/10.3389/fimmu.2019.02549>
Amelie Trinquand et al.,
*Towards molecular stratification of pediatric T-cell lymphoblastic lymphomas based on Minimal Disseminated Disease and NOTCH1/FBXW7 mutational status: the French EURO-LB02 experience (preprint)*
*Towards molecular stratification of pediatric T-cell lymphoblastic lymphomas based on Minimal Disseminated Disease and NOTCH1/FBXW7 mutational status: the French EURO-LB02 experience (preprint)*,
medRxiv 2020.09.08.20189829,
<https://www.medrxiv.org/content/10.1101/2020.09.08.20189829v1>
......@@ -224,11 +239,11 @@ Pediatric Blood & Cancer, 2019,
<https://doi.org/10.1002/pbc.27787>
Wen‐Qing Yao et al.,
*Angioimmunoblastic T‐cell lymphoma contains multiple clonal T‐cell populations derived from a common TET2 mutant progenitor cell*
*Angioimmunoblastic T‐cell lymphoma contains multiple clonal T‐cell populations derived from a common TET2 mutant progenitor cell*,
The Journal of Pathology, 2019,
<https://doi.org/10.1002/path.5376>
Yasuda et al.,
*Clinical utility of target capture‐based panel sequencing in hematological malignancies: A multicenter feasibility study*
*Clinical utility of target capture‐based panel sequencing in hematological malignancies: A multicenter feasibility study*,
Cancer Science, 2020, 111(9):3367-3378,
<https://dx.doi.org/10.1111/cas.14552>
# vidjil-algo 2021.02
# vidjil-algo 2021.02.2
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
......
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